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Rudenko V, Korotkov E. Study of Dispersed Repeats in the Cyanidioschyzon merolae Genome. Int J Mol Sci 2024; 25:4441. [PMID: 38674025 PMCID: PMC11050394 DOI: 10.3390/ijms25084441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we applied the iterative procedure (IP) method to search for families of highly diverged dispersed repeats in the genome of Cyanidioschyzon merolae, which contains over 16 million bases. The algorithm included the construction of position weight matrices (PWMs) for repeat families and the identification of more dispersed repeats based on the PWMs using dynamic programming. The results showed that the C. merolae genome contained 20 repeat families comprising a total of 33,938 dispersed repeats, which is significantly more than has been previously found using other methods. The repeats varied in length from 108 to 600 bp (522.54 bp in average) and occupied more than 72% of the C. merolae genome, whereas previously identified repeats, including tandem repeats, have been shown to constitute only about 28%. The high genomic content of dispersed repeats and their location in the coding regions suggest a significant role in the regulation of the functional activity of the genome.
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Affiliation(s)
- Valentina Rudenko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia;
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2
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Jacob DR, Guiblet WM, Mamayusupova H, Shtumpf M, Ciuta I, Ruje L, Gretton S, Bikova M, Correa C, Dellow E, Agrawal SP, Shafiei N, Drobysevskaja A, Armstrong CM, Lam JDG, Vainshtein Y, Clarkson CT, Thorn GJ, Sohn K, Pradeepa MM, Chandrasekharan S, Brooke GN, Klenova E, Zhurkin VB, Teif VB. Nucleosome reorganisation in breast cancer tissues. Clin Epigenetics 2024; 16:50. [PMID: 38561804 PMCID: PMC10986098 DOI: 10.1186/s13148-024-01656-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Nucleosome repositioning in cancer is believed to cause many changes in genome organisation and gene expression. Understanding these changes is important to elucidate fundamental aspects of cancer. It is also important for medical diagnostics based on cell-free DNA (cfDNA), which originates from genomic DNA regions protected from digestion by nucleosomes. RESULTS We have generated high-resolution nucleosome maps in paired tumour and normal tissues from the same breast cancer patients using MNase-assisted histone H3 ChIP-seq and compared them with the corresponding cfDNA from blood plasma. This analysis has detected single-nucleosome repositioning at key regulatory regions in a patient-specific manner and common cancer-specific patterns across patients. The nucleosomes gained in tumour versus normal tissue were particularly informative of cancer pathways, with ~ 20-fold enrichment at CpG islands, a large fraction of which marked promoters of genes encoding DNA-binding proteins. The tumour tissues were characterised by a 5-10 bp decrease in the average distance between nucleosomes (nucleosome repeat length, NRL), which is qualitatively similar to the differences between pluripotent and differentiated cells. This effect was correlated with gene activity, differential DNA methylation and changes in local occupancy of linker histone variants H1.4 and H1X. CONCLUSIONS Our study offers a novel resource of high-resolution nucleosome maps in breast cancer patients and reports for the first time the effect of systematic decrease of NRL in paired tumour versus normal breast tissues from the same patient. Our findings provide a new mechanistic understanding of nucleosome repositioning in tumour tissues that can be valuable for patient diagnostics, stratification and monitoring.
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Affiliation(s)
- Divya R Jacob
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Wilfried M Guiblet
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hulkar Mamayusupova
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Mariya Shtumpf
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Isabella Ciuta
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Luminita Ruje
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Svetlana Gretton
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
- School of Engineering, Arts, Science and Technology, University of Suffolk, James Hehir Building, University Avenue, Ipswich, Suffolk, IP3 0FS, UK
| | - Milena Bikova
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Clark Correa
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Emily Dellow
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Shivam P Agrawal
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Navid Shafiei
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | | | - Chris M Armstrong
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan D G Lam
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Yevhen Vainshtein
- Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB, Nobelstraße 12, 70569, Stuttgart, Germany
| | - Christopher T Clarkson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
- University College London, Gower St, Bloomsbury, London, WC1E 6BT, UK
| | - Graeme J Thorn
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Kai Sohn
- Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB, Nobelstraße 12, 70569, Stuttgart, Germany
| | - Madapura M Pradeepa
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Sankaran Chandrasekharan
- Colchester General Hospital, East Suffolk and North Essex NHS Foundation Trust, Turner Road, Colchester, CO4 5JL, UK
| | - Greg N Brooke
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Elena Klenova
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Victor B Zhurkin
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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3
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Salafranca J, Ko JK, Mukherjee AK, Fritzsche M, van Grinsven E, Udalova IA. Neutrophil nucleus: shaping the past and the future. J Leukoc Biol 2023; 114:585-594. [PMID: 37480361 PMCID: PMC10673716 DOI: 10.1093/jleuko/qiad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023] Open
Abstract
Neutrophils are innate immune cells that are key to protecting the host against infection and maintaining body homeostasis. However, if dysregulated, they can contribute to disease, such as in cancer or chronic autoinflammatory disorders. Recent studies have highlighted the heterogeneity in the neutrophil compartment and identified the presence of immature neutrophils and their precursors in these pathologies. Therefore, understanding neutrophil maturity and the mechanisms through which they contribute to disease is critical. Neutrophils were first characterized morphologically by Ehrlich in 1879 using microscopy, and since then, different technologies have been used to assess neutrophil maturity. The advances in the imaging field, including state-of-the-art microscopy and machine learning algorithms for image analysis, reinforce the use of neutrophil nuclear morphology as a fundamental marker of maturity, applicable for objective classification in clinical diagnostics. New emerging approaches, such as the capture of changes in chromatin topology, will provide mechanistic links between the nuclear shape, chromatin organization, and transcriptional regulation during neutrophil maturation.
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Affiliation(s)
- Julia Salafranca
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jacky Ka Ko
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Ananda K Mukherjee
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Marco Fritzsche
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Erinke van Grinsven
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Irina A Udalova
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
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Piroeva KV, McDonald C, Xanthopoulos C, Fox C, Clarkson CT, Mallm JP, Vainshtein Y, Ruje L, Klett LC, Stilgenbauer S, Mertens D, Kostareli E, Rippe K, Teif VB. Nucleosome repositioning in chronic lymphocytic leukemia. Genome Res 2023; 33:1649-1661. [PMID: 37699659 PMCID: PMC10691546 DOI: 10.1101/gr.277298.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/07/2023] [Indexed: 09/14/2023]
Abstract
The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we conducted a genome-wide comparison of high-resolution nucleosome maps in peripheral blood B cells from patients with chronic lymphocytic leukemia (CLL) and healthy individuals at single-base-pair resolution. Our investigation uncovered significant changes of nucleosome positioning in CLL. Globally, the spacing between nucleosomes-the nucleosome repeat length (NRL)-is shortened in CLL. This effect is stronger in the more aggressive IGHV-unmutated CLL subtype than in the IGHV-mutated CLL subtype. Changes in nucleosome occupancy at specific sites are linked to active chromatin remodeling and reduced DNA methylation. Nucleosomes lost or gained in CLL marks differential binding of 3D chromatin organizers such as CTCF as well as immune response-related transcription factors and delineated mechanisms of epigenetic deregulation. The principal component analysis of nucleosome occupancy in cancer-specific regions allowed the classification of samples between cancer subtypes and normal controls. Furthermore, patients could be better assigned to CLL subtypes according to differential nucleosome occupancy than based on DNA methylation or gene expression. Thus, nucleosome positioning constitutes a novel readout to dissect molecular mechanisms of disease progression and to stratify patients. Furthermore, we anticipate that the global nucleosome repositioning detected in our study, such as changes in the NRL, can be exploited for liquid biopsy applications based on cell-free DNA to stratify patients and monitor disease progression.
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Affiliation(s)
- Kristan V Piroeva
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Charlotte McDonald
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Charalampos Xanthopoulos
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Chelsea Fox
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Christopher T Clarkson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Jan-Philipp Mallm
- German Cancer Research Center (DKFZ) Heidelberg, Single Cell Open Lab, 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, 69120 Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany
| | - Yevhen Vainshtein
- Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB, 70569 Stuttgart, Germany
| | - Luminita Ruje
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Lara C Klett
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, 69120 Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany
| | - Stephan Stilgenbauer
- Division of CLL, University Hospital Ulm, Department of Internal Medicine III, 89081 Ulm, Germany
| | - Daniel Mertens
- Division of CLL, University Hospital Ulm, Department of Internal Medicine III, 89081 Ulm, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Cooperation Unit Mechanisms of Leukemogenesis, 69120 Heidelberg, Germany
| | - Efterpi Kostareli
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom;
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, 69120 Heidelberg, Germany;
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom;
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5
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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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6
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Sharma R, Pandey N, Mongia A, Mishra S, Majumdar A, Kumar V. FITs: forest of imputation trees for recovering true signals in single-cell open chromatin profiles. NAR Genom Bioinform 2020; 2:lqaa091. [PMID: 33575635 PMCID: PMC7676476 DOI: 10.1093/nargab/lqaa091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/13/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022] Open
Abstract
The advent of single-cell open-chromatin profiling technology has facilitated the analysis of heterogeneity of activity of regulatory regions at single-cell resolution. However, stochasticity and availability of low amount of relevant DNA, cause high drop-out rate and noise in single-cell open-chromatin profiles. We introduce here a robust method called as forest of imputation trees (FITs) to recover original signals from highly sparse and noisy single-cell open-chromatin profiles. FITs makes multiple imputation trees to avoid bias during the restoration of read-count matrices. It resolves the challenging issue of recovering open chromatin signals without blurring out information at genomic sites with cell-type-specific activity. Besides visualization and classification, FITs-based imputation also improved accuracy in the detection of enhancers, calculating pathway enrichment score and prediction of chromatin-interactions. FITs is generalized for wider applicability, especially for highly sparse read-count matrices. The superiority of FITs in recovering signals of minority cells also makes it highly useful for single-cell open-chromatin profile from in vivo samples. The software is freely available at https://reggenlab.github.io/FITs/.
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Affiliation(s)
- Rachesh Sharma
- Department of Electronic and Communication Engineering, Indraprastha Institute of Information Technology Delhi, Okhla Industrial Estate, Phase-III, New Delhi 110020, India
| | - Neetesh Pandey
- Department of Computational Biology, Indraprastha Institute of Information Technology Delhi, Okhla Industrial Estate, Phase-III, New Delhi 110020, India
| | - Aanchal Mongia
- Department of Electronic and Communication Engineering, Indraprastha Institute of Information Technology Delhi, Okhla Industrial Estate, Phase-III, New Delhi 110020, India
| | - Shreya Mishra
- Department of Computational Biology, Indraprastha Institute of Information Technology Delhi, Okhla Industrial Estate, Phase-III, New Delhi 110020, India
| | - Angshul Majumdar
- Department of Electronic and Communication Engineering, Indraprastha Institute of Information Technology Delhi, Okhla Industrial Estate, Phase-III, New Delhi 110020, India
| | - Vibhor Kumar
- Department of Computational Biology, Indraprastha Institute of Information Technology Delhi, Okhla Industrial Estate, Phase-III, New Delhi 110020, India
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Wierzchowski K, Grabowska I, Pilarek M. Efficient propagation of suspended HL-60 cells in a disposable bioreactor supporting wave-induced agitation at various Reynolds number. Bioprocess Biosyst Eng 2020; 43:1973-1985. [PMID: 32519077 PMCID: PMC7511289 DOI: 10.1007/s00449-020-02386-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/29/2020] [Indexed: 11/26/2022]
Abstract
Growth of human nonadherent HL-60 cell cultures performed in disposable bioreactor under various hydrodynamic conditions of 2-D wave-assisted agitation has been compared and discussed. Influence of Reynolds number for liquid (ReL) and the kLa coefficient, as key parameters characterized the bioprocessing of HL-60 cells in ReadyToProcess WAVETM 25 system, on reached values of the apparent maximal specific growth rate (μmax) and the specific yield of biomass (Y*X/S) has been identified. The values of ReL (i.e., 510–10,208), as well as kLa coefficient (i.e., 2.83–13.55 h−1), have been estimated for the cultures subjected to wave-induced mixing, based on simplified dimensionless correlation for various presents of WAVE 25 system. The highest values of apparent μmax = 0.038 h−1 and Y*X/S = 25.64 × 108 cells gglc−1 have been noted for cultures independently performed at wave-induced agitation characterized by ReL equaled to 5104 and 510, respectively. The presented results have high applicability potential in scale-up of bioprocesses focused on nonadherent animal cells, or in the case of any application of disposable bioreactors presenting similitude.
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Affiliation(s)
- Kamil Wierzchowski
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Waryńskiego 1, 00-645, Warsaw, Poland
| | - Iwona Grabowska
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Maciej Pilarek
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Waryńskiego 1, 00-645, Warsaw, Poland.
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Teif VB, Gould TJ, Clarkson CT, Boyd L, Antwi EB, Ishaque N, Olins AL, Olins DE. Linker histone epitopes are hidden by in situ higher-order chromatin structure. Epigenetics Chromatin 2020; 13:26. [PMID: 32505195 PMCID: PMC7276084 DOI: 10.1186/s13072-020-00345-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone H1 is the most mobile histone in the cell nucleus. Defining the positions of H1 on chromatin in situ, therefore, represents a challenge. Immunoprecipitation of formaldehyde-fixed and sonicated chromatin, followed by DNA sequencing (xChIP-seq), is traditionally the method for mapping histones onto DNA elements. But since sonication fragmentation precedes ChIP, there is a consequent loss of information about chromatin higher-order structure. Here, we present a new method, xxChIP-seq, employing antibody binding to fixed intact in situ chromatin, followed by extensive washing, a second fixation, sonication and immunoprecipitation. The second fixation is intended to prevent the loss of specifically bound antibody during washing and subsequent sonication and to prevent antibody shifting to epitopes revealed by the sonication process. In many respects, xxChIP-seq is comparable to immunostaining microscopy, which also involves interaction of the primary antibody with fixed and permeabilized intact cells. The only epitopes displayed after immunostaining are the "exposed" epitopes, not "hidden" by the fixation of chromatin higher-order structure. Comparison of immunoprecipitated fragments between xChIP-seq versus xxChIP-seq should indicate which epitopes become inaccessible with fixation and identify their associated DNA elements. RESULTS We determined the genomic distribution of histone variants H1.2 and H1.5 in human myeloid leukemia cells HL-60/S4 and compared their epitope exposure by both xChIP-seq and xxChIP-seq, as well as high-resolution microscopy, illustrating the influences of preserved chromatin higher-order structure in situ. We found that xChIP and xxChIP H1 signals are in general negatively correlated, with differences being more pronounced near active regulatory regions. Among the intriguing observations, we find that transcription-related regions and histone PTMs (i.e., enhancers, promoters, CpG islands, H3K4me1, H3K4me3, H3K9ac, H3K27ac and H3K36me3) exhibit significant deficiencies (depletions) in H1.2 and H1.5 xxChIP-seq reads, compared to xChIP-seq. These observations suggest the existence of in situ transcription-related chromatin higher-order structures stabilized by formaldehyde. CONCLUSION Comparison of H1 xxChIP-seq to H1 xChIP-seq allows the development of hypotheses on the chromosomal localization of (stabilized) higher-order structure, indicated by the generation of "hidden" H1 epitopes following formaldehyde crosslinking. Changes in H1 epitope exposure surrounding averaged chromosomal binding sites or epigenetic modifications can also indicate whether these sites have chromatin higher-order structure. For example, comparison between averaged active or inactive promoter regions suggests that both regions can acquire stabilized higher-order structure with hidden H1 epitopes. However, the H1 xChIP-seq comparison cannot define their differences. Application of the xxChIP-seq versus H1 xChIP-seq method is particularly relevant to chromatin-associated proteins, such as linker histones, that play dynamic roles in establishing chromatin higher-order structure.
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Affiliation(s)
- Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Travis J Gould
- Department of Physics & Astronomy, Bates College, Lewiston, ME, USA
| | | | - Logan Boyd
- Department of Physics & Astronomy, Bates College, Lewiston, ME, USA.,StarBird Technologies, LLC, Brunswick, ME, USA
| | - Enoch B Antwi
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Molecular and Cellular Engineering, Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, Freiburg im Breisgau, 79104 , Germany
| | - Naveed Ishaque
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, Berlin, 10178 , Germany
| | - Ada L Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME, 04103, USA
| | - Donald E Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME, 04103, USA.
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9
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Antwi EB, Olins A, Teif VB, Bieg M, Bauer T, Gu Z, Brors B, Eils R, Olins D, Ishaque N. Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. Biol Open 2020; 9:bio044222. [PMID: 31988093 PMCID: PMC7044446 DOI: 10.1242/bio.044222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 01/13/2020] [Indexed: 12/22/2022] Open
Abstract
Epigenomic regulation plays a vital role in cell differentiation. The leukemic HL-60/S4 [human myeloid leukemic cell line HL-60/S4 (ATCC CRL-3306)] promyelocytic cell can be easily differentiated from its undifferentiated promyelocyte state into neutrophil- and macrophage-like cell states. In this study, we present the underlying genome and epigenome architecture of HL-60/S4 through its differentiation. We performed whole-genome bisulphite sequencing of HL-60/S4 cells and their differentiated counterparts. With the support of karyotyping, we show that HL-60/S4 maintains a stable genome throughout differentiation. Analysis of differential Cytosine-phosphate-Guanine dinucleotide methylation reveals that most methylation changes occur in the macrophage-like state. Differential methylation of promoters was associated with immune-related terms. Key immune genes, CEBPA, GFI1, MAFB and GATA1 showed differential expression and methylation. However, we observed the strongest enrichment of methylation changes in enhancers and CTCF binding sites, implying that methylation plays a major role in large-scale transcriptional reprogramming and chromatin reorganisation during differentiation. Correlation of differential expression and distal methylation with support from chromatin capture experiments allowed us to identify putative proximal and long-range enhancers for a number of immune cell differentiation genes, including CEBPA and CCNF Integrating expression data, we present a model of HL-60/S4 differentiation in relation to the wider scope of myeloid differentiation.
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Affiliation(s)
- Enoch B Antwi
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular and Cellular Engineering, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg, Germany
| | - Ada Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, USA
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Colchester, UK
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
- Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
| | - Tobias Bauer
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Core Center, Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
- Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
| | - Donald Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, USA
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
- Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
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10
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Erenpreisa J, Giuliani A. Resolution of Complex Issues in Genome Regulation and Cancer Requires Non-Linear and Network-Based Thermodynamics. Int J Mol Sci 2019; 21:E240. [PMID: 31905791 PMCID: PMC6981914 DOI: 10.3390/ijms21010240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/22/2019] [Accepted: 12/27/2019] [Indexed: 02/06/2023] Open
Abstract
The apparent lack of success in curing cancer that was evidenced in the last four decades of molecular medicine indicates the need for a global re-thinking both its nature and the biological approaches that we are taking in its solution. The reductionist, one gene/one protein method that has served us well until now, and that still dominates in biomedicine, requires complementation with a more systemic/holistic approach, to address the huge problem of cross-talk between more than 20,000 protein-coding genes, about 100,000 protein types, and the multiple layers of biological organization. In this perspective, the relationship between the chromatin network organization and gene expression regulation plays a fundamental role. The elucidation of such a relationship requires a non-linear thermodynamics approach to these biological systems. This change of perspective is a necessary step for developing successful 'tumour-reversion' therapeutic strategies.
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Affiliation(s)
- Jekaterina Erenpreisa
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Alessandro Giuliani
- Environmental and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy;
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11
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Erenpreisa J, Krigerts J, Salmina K, Selga T, Sorokins H, Freivalds T. Differential staining of peripheral nuclear chromatin with Acridine orange implies an A-form epichromatin conformation of the DNA. Nucleus 2019; 9:171-181. [PMID: 29363398 PMCID: PMC5973139 DOI: 10.1080/19491034.2018.1431081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The chromatin observed by conventional electron microscopy under the nuclear envelope constitutes a single layer of dense 30–35 nm granules, while ∼30 nm fibrils laterally attached to them, form large patches of lamin-associated domains (LADs). This particular surface “epichromatin” can be discerned by specific (H2A+H2B+DNA) conformational antibody at the inner nuclear envelope and around mitotic chromosomes. In order to differentiate the DNA conformation of the peripheral chromatin we applied an Acridine orange (AO) DNA structural test involving RNAse treatment and the addition of AO after acid pre-treatment. MCF-7 cells treated in this way revealed yellow/red patches of LADs attached to a thin green nuclear rim and with mitotic chromosomes outlined in green, topologically corresponding to epichromatin epitope staining by immunofluorescence. Differentially from LADs, the epichromatin was unable to provide metachromatic staining by AO, unless thermally denatured at 94oC. DNA enrichment in GC stretches has been recently reported for immunoprecipitated ∼ 1Kb epichromatin domains. Together these data suggest that certain epichromatin segments assume the relatively hydrophobic DNA A-conformation at the nuclear envelope and surface of mitotic chromosomes, preventing AO side dimerisation. We hypothesize that epichromatin domains form nucleosome superbeads. Hydrophobic interactions stack these superbeads and align them at the nuclear envelope, while repulsing the hydrophilic LADs. The hydrophobicity of epichromatin explains its location at the surface of mitotic chromosomes and its function in mediating chromosome attachment to the restituting nuclear envelope during telophase.
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Affiliation(s)
| | - Jekabs Krigerts
- a Latvian Biomedical Research & Study Centre , Ratsupites 1, Riga , Latvia.,b Institute of Biomedical Engineering and Nanotechnologies, Riga Technical University , Kalku iela 1, Riga , Latvia
| | - Kristine Salmina
- a Latvian Biomedical Research & Study Centre , Ratsupites 1, Riga , Latvia
| | - Turs Selga
- c Faculty of Biology, University of Latvia , Raina bulvaris 19, Riga , Latvia
| | - Hermanis Sorokins
- b Institute of Biomedical Engineering and Nanotechnologies, Riga Technical University , Kalku iela 1, Riga , Latvia
| | - Talivaldis Freivalds
- d Institute of Kardiology and Regenerative Medicine, University of Latvia , Raina bulvaris 19, Riga , Latvia
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12
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Harwood JC, Kent NA, Allen ND, Harwood AJ. Nucleosome dynamics of human iPSC during neural differentiation. EMBO Rep 2019; 20:embr.201846960. [PMID: 31036712 PMCID: PMC6549019 DOI: 10.15252/embr.201846960] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 01/07/2023] Open
Abstract
Nucleosome positioning is important for neurodevelopment, and genes mediating chromatin remodelling are strongly associated with human neurodevelopmental disorders. To investigate changes in nucleosome positioning during neural differentiation, we generate genome‐wide nucleosome maps from an undifferentiated human‐induced pluripotent stem cell (hiPSC) line and after its differentiation to the neural progenitor cell (NPC) stage. We find that nearly 3% of nucleosomes are highly positioned in NPC, but significantly, there are eightfold fewer positioned nucleosomes in pluripotent cells, indicating increased positioning during cell differentiation. Positioned nucleosomes do not strongly correlate with active chromatin marks or gene transcription. Unexpectedly, we find a small population of nucleosomes that occupy similar positions in pluripotent and neural progenitor cells and are found at binding sites of the key gene regulators NRSF/REST and CTCF. Remarkably, the presence of these nucleosomes appears to be independent of the associated regulatory complexes. Together, these results present a scenario in human cells, where positioned nucleosomes are sparse and dynamic, but may act to alter gene expression at a distance via the structural conformation at sites of chromatin regulation.
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Affiliation(s)
- Janet C Harwood
- MRC Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | | | | | - Adrian J Harwood
- School of Biosciences, Cardiff University, Cardiff, UK .,Neuroscience and Mental Health Research Institute (NMHRI), Cardiff University, Cardiff, UK
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13
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Olins DE, Olins AL. Epichromatin and chromomeres: a 'fuzzy' perspective. Open Biol 2019; 8:rsob.180058. [PMID: 29875200 PMCID: PMC6030114 DOI: 10.1098/rsob.180058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 05/09/2018] [Indexed: 12/17/2022] Open
Abstract
'Epichromatin', the surface of chromatin beneath the interphase nuclear envelope (NE) or at the surface of mitotic chromosomes, was discovered by immunostaining with a specific bivalent mouse monoclonal anti-nucleosome antibody (mAb PL2-6). 'Chromomeres', punctate chromatin particles approximately 200-300 nm in diameter, identified throughout the interphase chromatin and along mitotic chromosomes, were observed by immunostaining with the monovalent papain-derived Fab fragments of bivalent PL2-6. The specific target for PL2-6 appears to include the nucleosome acidic patch. Thus, within the epichromatin and chromomeric regions, this epitope is 'exposed'. Considering that histones possess unstructured 'tails' (i.e. intrinsically disordered peptide regions, IDPR), our perception of these chromatin regions becomes more 'fuzzy' (less defined). We suggest that epichromatin cationic tails facilitate interactions with anionic components of NE membranes. We also suggest that the unstructured histone tails (especially, histone H1 tails), with their presumed promiscuous binding, establish multivalent binding that stabilizes each chromomere as a unit of chromatin higher order structure. We propose an 'unstructured stability' hypothesis, which postulates that the stability of epichromatin and chromomeres (as well as other nuclear chromatin structures) is a consequence of the collective contributions of numerous weak histone IDPR binding interactions arising from the multivalent nucleosome, analogous to antibody avidity.
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Affiliation(s)
- Donald E Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
| | - Ada L Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
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14
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Chirico G, Gansen A, Leuba SH, Olins AL, Olins DE, Smith JC, Tóth K. Jörg Langowski: his scientific legacy and the future it promises. BMC BIOPHYSICS 2018; 11:5. [PMID: 30026939 PMCID: PMC6048899 DOI: 10.1186/s13628-018-0045-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/27/2018] [Indexed: 11/10/2022]
Abstract
Background With the passing of Jörg Langowski 6 May 2017 in a sailplane accident, the scientific community was deprived of a strident and effective voice for DNA and chromatin molecular and computational biophysics, for open access publishing and for the creation of effective scientific research networks. Methods Here, after reviewing some of Jörg's key research contributions and ideas, we offer through the personal remembrance of his closest collaborators, a deep analysis of the major results of his research and the future directions they have engendered. Conclusions The legacy of Jörg Langowski has been to propel a way of viewing biological function that considers living systems as dynamic and in three dimensions. This physical view of biology that he pioneered is now, finally, becoming established also because of his great effort.
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Affiliation(s)
- Giuseppe Chirico
- 1Dipartimento di Fisica, Università di Milano-Bicocca, Milan, Italy
| | - Alexander Gansen
- 2Biophysics of Macromolecules (B040), Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sanford H Leuba
- 3Departments of Cell Biology and Bioengineering, 2.26a UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Ada L Olins
- 4Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME USA
| | - Donald E Olins
- 4Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME USA
| | - Jeremy C Smith
- 5Oak Ridge National Laboratory, P.O. Box 2008 MS6309, Oak Ridge, TN 37831-6309 USA.,6Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
| | - Katalin Tóth
- 2Biophysics of Macromolecules (B040), Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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15
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Iteratively improving Hi-C experiments one step at a time. Methods 2018; 142:47-58. [DOI: 10.1016/j.ymeth.2018.04.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/01/2018] [Accepted: 04/25/2018] [Indexed: 02/03/2023] Open
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16
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Gould TJ, Tóth K, Mücke N, Langowski J, Hakusui AS, Olins AL, Olins DE. Defining the epichromatin epitope. Nucleus 2017; 8:625-640. [PMID: 28960120 DOI: 10.1080/19491034.2017.1380141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Epichromatin is identified by immunostaining fixed and permeabilized cells with particular bivalent anti-nucleosome antibodies (mAbs PL2-6 and 1H6). During interphase, epichromatin resides adjacent to the inner nuclear membrane; during mitosis, at the outer surface of mitotic chromosomes. By STED (stimulated emission depletion) microscopy, PL2-6 stained interphase epichromatin is ∼76 nm thick and quite uniform; mitotic epichromatin is more variable in thickness, exhibiting a "wrinkled" surface with an average thickness of ∼78 nm. Co-immunostaining with anti-Ki-67 demonstrates Ki-67 deposition between the PL2-6 "ridges" of mitotic epichromatin. Monovalent papain-derived Fab fragments of PL2-6 yield a strikingly different punctate "chromomeric" immunostaining pattern throughout interphase nuclei and along mitotic chromosome arms. Evidence from electrophoretic mobility shift assay (EMSA) and from analytical ultracentrifugation characterize the Fab/mononucleosome complex, supporting the concept that there are two binding sites per nucleosome. The peptide sequence of the Hv3 region (heavy chain variable region 3) of the PL2-6 antibody binding site strongly resembles other nucleosome acidic patch binding proteins (especially, LANA and CENPC), supporting that the nucleosome acidic patch is included within the epichromatin epitope. It is speculated that the interphase epichromatin epitope is "exposed" with favorable geometric arrangements for binding bivalent PL2-6 at the surface chromatin; whereas, the epitope is "hidden" within internal chromatin. Furthermore, it is suggested that the "exposed" nucleosome surface of mitotic epichromatin may play a role in post-mitotic nuclear envelope reformation.
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Affiliation(s)
- Travis J Gould
- a Department of Physics & Astronomy , Bates College , Lewiston , ME , USA
| | - Katalin Tóth
- b Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Norbert Mücke
- b Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jörg Langowski
- b Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | | | - Ada L Olins
- c Department of Pharmaceutical Sciences , College of Pharmacy, University of New England , Portland , ME , USA
| | - Donald E Olins
- c Department of Pharmaceutical Sciences , College of Pharmacy, University of New England , Portland , ME , USA
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