2
|
Hill SL, Rogan PK, Wang YX, Knoll JHM. Differentially accessible, single copy sequences form contiguous domains along metaphase chromosomes that are conserved among multiple tissues. Mol Cytogenet 2021; 14:49. [PMID: 34670606 PMCID: PMC8527651 DOI: 10.1186/s13039-021-00567-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND During mitosis, chromatin engages in a dynamic cycle of condensation and decondensation. Condensation into distinct units to ensure high fidelity segregation is followed by rapid and reproducible decondensation to produce functional daughter cells. Factors contributing to the reproducibility of chromatin structure between cell generations are not well understood. We investigated local metaphase chromosome condensation along mitotic chromosomes within genomic intervals showing differential accessibility (DA) between homologs. DA was originally identified using short sequence-defined single copy (sc) DNA probes of < 5 kb in length by fluorescence in situ hybridization (scFISH) in peripheral lymphocytes. These structural differences between metaphase homologs are non-random, stable, and heritable epigenetic marks which have led to the proposed function of DA as a marker of chromatin memory. Here, we characterize the organization of DA intervals into chromosomal domains by identifying multiple DA loci in close proximity to each other and examine the conservation of DA between tissues. RESULTS We evaluated multiple adjacent scFISH probes at 6 different DA loci from chromosomal regions 2p23, 3p24, 12p12, 15q22, 15q24 and 20q13 within peripheral blood T-lymphocytes. DA was organized within domains that extend beyond the defined boundaries of individual scFISH probes. Based on hybridizations of 2 to 4 scFISH probes per domain, domains ranged in length from 16.0 kb to 129.6 kb. Transcriptionally inert chromosomal DA regions in T-lymphocytes also demonstrated conservation of DA in bone marrow and fibroblast cells. CONCLUSIONS We identified novel chromosomal regions with allelic differences in metaphase chromosome accessibility and demonstrated that these accessibility differences appear to be aggregated into contiguous domains extending beyond individual scFISH probes. These domains are encompassed by previously established topologically associated domain (TAD) boundaries. DA appears to be a conserved feature of human metaphase chromosomes across different stages of lymphocyte differentiation and germ cell origin, consistent with its proposed role in maintenance of intergenerational cellular chromosome memory.
Collapse
Affiliation(s)
- Seana L Hill
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
| | - Peter K Rogan
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
- Cytognomix Inc., London, ON, Canada
| | - Yi Xuan Wang
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
| | - Joan H M Knoll
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada.
- Cytognomix Inc., London, ON, Canada.
| |
Collapse
|
3
|
Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet 2018; 14:e1007872. [PMID: 30586358 PMCID: PMC6324821 DOI: 10.1371/journal.pgen.1007872] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/08/2019] [Accepted: 12/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chromosome organization is crucial for genome function. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Focusing on chromosomal regions that contribute to compartments, we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Imaging through the depths of entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method-integrative modeling of genomic regions (IMGR)-to increase the genomic resolution of our traces to 10 kb.
Collapse
MESH Headings
- Cells, Cultured
- Chromosome Painting/methods
- Chromosome Structures/chemistry
- Chromosome Structures/genetics
- Chromosome Structures/ultrastructure
- Chromosome Walking/methods
- Chromosomes, Human, Pair 19/chemistry
- Chromosomes, Human, Pair 19/genetics
- Chromosomes, Human, Pair 19/ultrastructure
- Female
- Fluorescent Dyes
- Humans
- Imaging, Three-Dimensional
- In Situ Hybridization, Fluorescence/methods
- Male
- Models, Genetic
- Oligonucleotide Probes
- Pedigree
Collapse
Affiliation(s)
- Guy Nir
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Irene Farabella
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cynthia Pérez Estrada
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - Carl G. Ebeling
- Bruker Nano Inc., Salt Lake City, Utah, United States of America
| | - Brian J. Beliveau
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Hiroshi M. Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Son C. Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shyamtanu Chattoraj
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jumana AlHaj Abed
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nuno M. C. Martins
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Huy Q. Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mohammed A. Hannan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sheikh Russell
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Neva C. Durand
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
| | - Suhas S. P. Rao
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jocelyn Y. Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paula Soler-Vila
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | | | | | - Jeff A. Stuckey
- Bruker Nano Inc., Middleton, Wisconsin, United States of America
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, United States of America
| | - Marc A. Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - C.-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| |
Collapse
|
4
|
Yu S, Yang F, Shen WH. Genome maintenance in the context of 4D chromatin condensation. Cell Mol Life Sci 2016; 73:3137-50. [PMID: 27098512 PMCID: PMC4956502 DOI: 10.1007/s00018-016-2221-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/07/2016] [Indexed: 12/20/2022]
Abstract
The eukaryotic genome is packaged in the three-dimensional nuclear space by forming loops, domains, and compartments in a hierarchical manner. However, when duplicated genomes prepare for segregation, mitotic cells eliminate topologically associating domains and abandon the compartmentalized structure. Alongside chromatin architecture reorganization during the transition from interphase to mitosis, cells halt most DNA-templated processes such as transcription and repair. The intrinsically condensed chromatin serves as a sophisticated signaling module subjected to selective relaxation for programmed genomic activities. To understand the elaborate genome-epigenome interplay during cell cycle progression, the steady three-dimensional genome requires a time scale to form a dynamic four-dimensional and a more comprehensive portrait. In this review, we will dissect the functions of critical chromatin architectural components in constructing and maintaining an orderly packaged chromatin environment. We will also highlight the importance of the spatially and temporally conscious orchestration of chromatin remodeling to ensure high-fidelity genetic transmission.
Collapse
Affiliation(s)
- Sonia Yu
- Department of Radiation Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY, 10065, USA
| | - Fan Yang
- Department of Radiation Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY, 10065, USA
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Wen H Shen
- Department of Radiation Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY, 10065, USA.
| |
Collapse
|
5
|
Khrustaleva L, Jiang J, Havey MJ. High-resolution tyramide-FISH mapping of markers tightly linked to the male-fertility restoration (Ms) locus of onion. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:535-545. [PMID: 26704420 DOI: 10.1007/s00122-015-2646-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
Tyramide FISH was used to locate relatively small genomic amplicons from molecular markers linked to Ms locus onto onion chromosome 2 near the centromere, a region of relatively low recombination. Fluorescence in situ hybridization (FISH) has not been readily exploited for physical mapping of molecular markers in plants due to the technical challenge of visualizing small single-copy probes. Signal amplification using tyramide (tyr) FISH can increase sensitivity up to 100-fold. We used tyr-FISH to physically locate molecular markers tightly linked to the nuclear male-fertility (Ms) restoration locus of onion onto mitotic metaphase, pachytene, and super-stretched pachytene chromosomes. Relatively short genomic amplicons (846-2251 bp) and a cDNA clone (666 bp) were visualized in 9-42 % of observed cells. The markers were assigned to proximal locations close to the centromere on the long arm of chromosome 2, a region of lower recombination, revealing that tightly linked markers may be physically distant from Ms. This result explains why several labs have identified molecular markers tightly linked to the Ms locus after screening relatively few DNA clones or primers and segregating progenies. Although these markers are still useful for marker-aided selection, our results indicate that map-based cloning of Ms will likely be difficult due to reduced recombination near this gene.
Collapse
Affiliation(s)
- Ludmila Khrustaleva
- Center of Molecular Biotechnology, Department of Genetics and Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, 49, Timiryazevskaya Str., 127550, Moscow, Russia.
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
| | - Michael J Havey
- USDA-ARS and Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
| |
Collapse
|
6
|
Khan WA, Rogan PK, Knoll JHM. Reversing chromatin accessibility differences that distinguish homologous mitotic metaphase chromosomes. Mol Cytogenet 2015; 8:65. [PMID: 26273322 PMCID: PMC4535684 DOI: 10.1186/s13039-015-0159-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromatin-modifying reagents that alter histone associating proteins, DNA conformation or its sequence are well established strategies for studying chromatin structure in interphase (G1, S, G2). Little is known about how these compounds act during metaphase. We assessed the effects of these reagents at genomic loci that show reproducible, non-random differences in accessibility to chromatin that distinguish homologous targets by single copy DNA probe fluorescence in situ hybridization (scFISH). By super-resolution 3-D structured illumination microscopy (3D-SIM) and other criteria, the differences correspond to 'differential accessibility' (DA) to these chromosomal regions. At these chromosomal loci, DA of the same homologous chromosome is stable and epigenetic hallmarks of less accessible interphase chromatin are present. RESULTS To understand the basis for DA, we investigate the impact of epigenetic modifiers on these allelic differences in chromatin accessibility between metaphase homologs in lymphoblastoid cell lines. Allelic differences in metaphase chromosome accessibility represent a stable chromatin mark on mitotic metaphase chromosomes. Inhibition of the topoisomerase IIα-DNA cleavage complex reversed DA. Inter-homolog probe fluorescence intensity ratios between chromosomes treated with ICRF-193 were significantly lower than untreated controls. 3D-SIM demonstrated that differences in hybridized probe volume and depth between allelic targets were equalized by this treatment. By contrast, DA was impervious to chromosome decondensation treatments targeting histone modifying enzymes, cytosine methylation, as well as in cells with regulatory defects in chromatid cohesion. These data altogether suggest that DA is a reflection of allelic differences in metaphase chromosome compaction, dictated by the localized catenation state of the chromosome, rather than by other epigenetic marks. CONCLUSIONS Inhibition of the topoisomerase IIα-DNA cleavage complex mitigated DA by decreasing DNA superhelicity and axial metaphase chromosome condensation. This has potential implications for the mechanism of preservation of cellular phenotypes that enables the same chromatin structure to be correctly reestablished in progeny cells of the same tissue or individual.
Collapse
Affiliation(s)
- Wahab A. Khan
- />Department of Pathology and Laboratory Medicine, University of Western Ontario, London, N6A 5C1 ON Canada
| | - Peter K. Rogan
- />Departments of Biochemistry, Computer Science, and Oncology, University of Western Ontario, London, N6A 5C1 ON Canada
- />Cytognomix, Inc., London, N6G 4X8 ON Canada
| | - Joan H. M. Knoll
- />Department of Pathology and Laboratory Medicine, University of Western Ontario, London, N6A 5C1 ON Canada
- />Cytognomix, Inc., London, N6G 4X8 ON Canada
| |
Collapse
|
7
|
Terrenoire E, Halsall JA, Turner BM. Immunolabelling of human metaphase chromosomes reveals the same banded distribution of histone H3 isoforms methylated at lysine 4 in primary lymphocytes and cultured cell lines. BMC Genet 2015; 16:44. [PMID: 25925961 PMCID: PMC4417270 DOI: 10.1186/s12863-015-0200-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/14/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Using metaphase spreads from human lymphoblastoid cell lines, we previously showed how immunofluorescence microscopy could define the distribution of histone modifications across metaphase chromosomes. We showed that different histone modifications gave consistent and clearly defined immunofluorescent banding patterns. However, it was not clear to what extent these higher level distributions were influenced by long-term growth in culture, or by the specific functional associations of individual histone modifications. RESULTS Metaphase chromosome spreads from human lymphocytes stimulated to grow in short-term culture, were immunostained with antibodies to histone H3 mono- or tri-methylated at lysine 4 (H3K4me1, H3K4me3). Chromosomes were identified on the basis of morphology and reverse DAPI (rDAPI) banding. Both antisera gave the same distinctive immunofluorescent staining pattern, with unstained heterochromatic regions and a banded distribution along the chromosome arms. Karyotypes were prepared, showing the reproducibility of banding between sister chromatids, homologue pairs and from one metaphase spread to another. At the light microscope level, we detect no difference between the banding patterns along chromosomes from primary lymphocytes and lymphoblastoid cell lines adapted to long-term growth in culture. CONCLUSIONS The distribution of H3K4me3 is the same across metaphase chromosomes from human primary lymphocytes and LCL, showing that higher level distribution is not altered by immortalization or long-term culture. The two modifications H3K4me1 (enriched in gene enhancer regions) and H3K4me3 (enriched in gene promoter regions) show the same distributions across human metaphase chromosomes, showing that functional differences do not necessarily cause modifications to differ in their higher-level distributions.
Collapse
Affiliation(s)
- Edith Terrenoire
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Mindelsohn Way, Edgbaston, Birmingham, B15 2TG, UK.
- Present address : Service de Génétique, CHU de Tours, 2 Boulevard Tonnellé, 37044, Tours, Cedex 09, France.
| | - John A Halsall
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Bryan M Turner
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| |
Collapse
|