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Mohanta TK, Mishra AK, Al-Harrasi A. The 3D Genome: From Structure to Function. Int J Mol Sci 2021; 22:11585. [PMID: 34769016 PMCID: PMC8584255 DOI: 10.3390/ijms222111585] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 01/09/2023] Open
Abstract
The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding factor domains, cohesin, and chromatin structures are the prominent identified components that encode the 3D structure of the genome. Although TADs are the major contributors to 3D genome organization, they are absent in Arabidopsis. However, a few research groups have reported the presence of TAD-like structures in the plant kingdom.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
| | - Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Korea; or
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
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2
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Genome-wide mapping of genomic DNA damage: methods and implications. Cell Mol Life Sci 2021; 78:6745-6762. [PMID: 34463773 PMCID: PMC8558167 DOI: 10.1007/s00018-021-03923-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 12/19/2022]
Abstract
Exposures from the external and internal environments lead to the modification of genomic DNA, which is implicated in the cause of numerous diseases, including cancer, cardiovascular, pulmonary and neurodegenerative diseases, together with ageing. However, the precise mechanism(s) linking the presence of damage, to impact upon cellular function and pathogenesis, is far from clear. Genomic location of specific forms of damage is likely to be highly informative in understanding this process, as the impact of downstream events (e.g. mutation, microsatellite instability, altered methylation and gene expression) on cellular function will be positional—events at key locations will have the greatest impact. However, until recently, methods for assessing DNA damage determined the totality of damage in the genomic location, with no positional information. The technique of “mapping DNA adductomics” describes the molecular approaches that map a variety of forms of DNA damage, to specific locations across the nuclear and mitochondrial genomes. We propose that integrated comparison of this information with other genome-wide data, such as mutational hotspots for specific genotoxins, tumour-specific mutation patterns and chromatin organisation and transcriptional activity in non-cancerous lesions (such as nevi), pre-cancerous conditions (such as polyps) and tumours, will improve our understanding of how environmental toxins lead to cancer. Adopting an analogous approach for non-cancer diseases, including the development of genome-wide assays for other cellular outcomes of DNA damage, will improve our understanding of the role of DNA damage in pathogenesis more generally.
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3
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Best NB, Addo-Quaye C, Kim BS, Weil CF, Schulz B, Johal G, Dilkes BP. Mutation of the nuclear pore complex component, aladin1, disrupts asymmetric cell division in Zea mays (maize). G3 GENES|GENOMES|GENETICS 2021; 11:6300521. [PMID: 36351283 PMCID: PMC8495933 DOI: 10.1093/g3journal/jkab106] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/17/2021] [Indexed: 11/17/2022]
Abstract
The nuclear pore complex (NPC) regulates the movement of macromolecules between the nucleus and cytoplasm. Dysfunction of many components of the NPC results in human genetic diseases, including triple A syndrome (AAAS) as a result of mutations in ALADIN. Here, we report a nonsense mutation in the maize ortholog, aladin1 (ali1-1), at the orthologous amino acid residue of an AAAS allele from humans, alters plant stature, tassel architecture, and asymmetric divisions of subsidiary mother cells (SMCs). Crosses with the stronger nonsense allele ali1-2 identified complex allele interactions for plant height and aberrant SMC division. RNA-seq analysis of the ali1-1 mutant identified compensatory transcript accumulation for other NPC components as well as gene expression consequences consistent with conservation of ALADIN1 functions between humans and maize. These findings demonstrate that ALADIN1 is necessary for normal plant development, shoot architecture, and asymmetric cell division in maize.
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Affiliation(s)
- Norman B Best
- Plant Genetics Research Unit, USDA, Agriculture Research Service, Columbia, MO 65211, USA
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Charles Addo-Quaye
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Natural Sciences and Mathematics Division, Lewis-Clark State College, Lewiston, ID 83501, USA
| | - Bong-Suk Kim
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Clifford F Weil
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Burkhard Schulz
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Guri Johal
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
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4
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Wheeler E, Brooks AM, Concia L, Vera DL, Wear EE, LeBlanc C, Ramu U, Vaughn MW, Bass HW, Martienssen RA, Thompson WF, Hanley-Bowdoin L. Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin. PLANT PHYSIOLOGY 2020; 183:206-220. [PMID: 32205451 PMCID: PMC7210620 DOI: 10.1104/pp.19.01520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/03/2020] [Indexed: 05/04/2023]
Abstract
The selection and firing of DNA replication origins play key roles in ensuring that eukaryotes accurately replicate their genomes. This process is not well documented in plants due in large measure to difficulties in working with plant systems. We developed a new functional assay to label and map very early replicating loci that must, by definition, include at least a subset of replication origins. Arabidopsis (Arabidopsis thaliana) cells were briefly labeled with 5-ethynyl-2'-deoxy-uridine, and nuclei were subjected to two-parameter flow sorting. We identified more than 5500 loci as initiation regions (IRs), the first regions to replicate in very early S phase. These were classified as strong or weak IRs based on the strength of their replication signals. Strong initiation regions were evenly spaced along chromosomal arms and depleted in centromeres, while weak initiation regions were enriched in centromeric regions. IRs are AT-rich sequences flanked by more GC-rich regions and located predominantly in intergenic regions. Nuclease sensitivity assays indicated that IRs are associated with accessible chromatin. Based on these observations, initiation of plant DNA replication shows some similarity to, but is also distinct from, initiation in other well-studied eukaryotic systems.
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Affiliation(s)
- Emily Wheeler
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
| | - Ashley M Brooks
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
| | - Lorenzo Concia
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
| | - Daniel L Vera
- Florida State University, Center for Genomics and Personalized Medicine, Tallahassee, Florida 32306
| | - Emily E Wear
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Umamaheswari Ramu
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Hank W Bass
- Florida State University, Department of Biological Science, Tallahassee, Florida 32306
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - William F Thompson
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
| | - Linda Hanley-Bowdoin
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
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5
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Dumur T, Duncan S, Graumann K, Desset S, Randall RS, Scheid OM, Prodanov D, Tatout C, Baroux C. Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions. Nucleus 2019; 10:181-212. [PMID: 31362571 PMCID: PMC6682351 DOI: 10.1080/19491034.2019.1644592] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. Abbreviations: 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel.
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Affiliation(s)
- Tao Dumur
- Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Susan Duncan
- Norwich Research Park, Earlham Institute, Norwich, UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Sophie Desset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont–Ferrand, France
| | - Ricardo S Randall
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Dimiter Prodanov
- Environment, Health and Safety, Neuroscience Research Flanders, Leuven, Belgium
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont–Ferrand, France
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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Shah MNA, Arabia S, Islam T, Ghosh A. Molecular evolution of SUN-domain containing proteins in diverse plant species and their expression profiling in response to developmental and perturbation stimuli. PHYTOCHEMISTRY 2019; 157:28-42. [PMID: 30359793 DOI: 10.1016/j.phytochem.2018.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 10/04/2018] [Accepted: 10/06/2018] [Indexed: 06/08/2023]
Abstract
SUN (Sad1/UNC-84) domain-containing proteins are highly conserved throughout evolution. They are localized to the inner membrane of the nuclear envelope and are involved in nuclear migration and nucleoskeleton formation. In the present study, a genome-wide investigation was performed in three dicotyledonous (Arabidopsis thaliana, Glycine max and Medicago truncatula) and three monocotyledonous (Oryza sativa, Zea mays and Sorghum bicolor) plants. A total of 56 SUN proteins encoded by 30 genes were identified. Based on their length, transmembrane topology, conserved domains and phylogenetic relationships, they could be divided into two previously defined groups- Cter-SUN and mid-SUN proteins. Expression of these genes was analyzed in different developmental stages, tissues and various unfavorable conditions such as salinity, drought, and hormonal treatment. Analyses indicated that the expression of SUN1/2 transcripts are ubiquitous; that of SUN3/4 are development/tissue regulated, and SUN5 are inflorescence stage-specific. This study provides an initial framework for the characterization and functional validation of the plant SUN family.
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Affiliation(s)
- Md Nur Ahad Shah
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Shatil Arabia
- Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Tahmina Islam
- Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
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7
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Concia L, Brooks AM, Wheeler E, Zynda GJ, Wear EE, LeBlanc C, Song J, Lee TJ, Pascuzzi PE, Martienssen RA, Vaughn MW, Thompson WF, Hanley-Bowdoin L. Genome-Wide Analysis of the Arabidopsis Replication Timing Program. PLANT PHYSIOLOGY 2018; 176:2166-2185. [PMID: 29301956 PMCID: PMC5841712 DOI: 10.1104/pp.17.01537] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/03/2018] [Indexed: 05/21/2023]
Abstract
Eukaryotes use a temporally regulated process, known as the replication timing program, to ensure that their genomes are fully and accurately duplicated during S phase. Replication timing programs are predictive of genomic features and activity and are considered to be functional readouts of chromatin organization. Although replication timing programs have been described for yeast and animal systems, much less is known about the temporal regulation of plant DNA replication or its relationship to genome sequence and chromatin structure. We used the thymidine analog, 5-ethynyl-2'-deoxyuridine, in combination with flow sorting and Repli-Seq to describe, at high-resolution, the genome-wide replication timing program for Arabidopsis (Arabidopsis thaliana) Col-0 suspension cells. We identified genomic regions that replicate predominantly during early, mid, and late S phase, and correlated these regions with genomic features and with data for chromatin state, accessibility, and long-distance interaction. Arabidopsis chromosome arms tend to replicate early while pericentromeric regions replicate late. Early and mid-replicating regions are gene-rich and predominantly euchromatic, while late regions are rich in transposable elements and primarily heterochromatic. However, the distribution of chromatin states across the different times is complex, with each replication time corresponding to a mixture of states. Early and mid-replicating sequences interact with each other and not with late sequences, but early regions are more accessible than mid regions. The replication timing program in Arabidopsis reflects a bipartite genomic organization with early/mid-replicating regions and late regions forming separate, noninteracting compartments. The temporal order of DNA replication within the early/mid compartment may be modulated largely by chromatin accessibility.
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Affiliation(s)
- Lorenzo Concia
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Ashley M Brooks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Emily Wheeler
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Gregory J Zynda
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas 78758
| | - Emily E Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas 78758
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Pete E Pascuzzi
- Purdue University Libraries, Purdue University, West Lafayette, Indiana 47907
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas 78758
| | - William F Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
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Groves NR, Biel AM, Newman-Griffis AH, Meier I. Dynamic Changes in Plant Nuclear Organization in Response to Environmental and Developmental Signals. PLANT PHYSIOLOGY 2018; 176:230-241. [PMID: 28739821 PMCID: PMC5761808 DOI: 10.1104/pp.17.00788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/17/2017] [Indexed: 05/19/2023]
Abstract
The functional organization of the plant nuclear pore, nuclear envelope, and nucleoplasm marks dynamically changing environmental cues and developmental programs.
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Affiliation(s)
- Norman R Groves
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Alecia M Biel
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Anna H Newman-Griffis
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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Breaking the scale: how disrupting the karyoplasmic ratio gives cancer cells an advantage for metastatic invasion. Biochem Soc Trans 2017; 45:1333-1344. [PMID: 29150524 DOI: 10.1042/bst20170153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/28/2017] [Accepted: 10/16/2017] [Indexed: 01/03/2023]
Abstract
Nuclear size normally scales with the size of the cell, but in cancer this 'karyoplasmic ratio' is disrupted. This is particularly so in more metastatic tumors where changes in the karyoplasmic ratio are used in both diagnosis and prognosis for several tumor types. However, the direction of nuclear size changes differs for particular tumor types: for example in breast cancer, larger nuclear size correlates with increased metastasis, while for lung cancer smaller nuclear size correlates with increased metastasis. Thus, there must be tissue-specific drivers of the nuclear size changes, but proteins thus far linked to nuclear size regulation are widely expressed. Notably, for these tumor types, ploidy changes have been excluded as the basis for nuclear size changes, and so, the increased metastasis is more likely to have a basis in the nuclear morphology change itself. We review what is known about nuclear size regulation and postulate how such nuclear size changes can increase metastasis and why the directionality can differ for particular tumor types.
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