1
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Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Pierno FD, Dekker J, Nicodemi M. Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603769. [PMID: 39071404 PMCID: PMC11275793 DOI: 10.1101/2024.07.16.603769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2Mb wide genomic region encompassing the human LTN1 gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in-silico the ensemble of single-molecule LTN1 3D structures, which we benchmark against recent in-situ Hi-C 2.0 data. The model-derived single molecules are then used to predict structural folding features at the single-cell level, providing testable predictions for super-resolution microscopy experiments.
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Affiliation(s)
- Mattia Conte
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Alex Abraham
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Liyan Yang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Johan H. Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Krishna M. Parsi
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655
| | - Francesca Vercellone
- DIETI, Università di Napoli Federico II, Via Claudio 21, 80125 Naples, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Andrea Fontana
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Florinda Di Pierno
- DIETI, Università di Napoli Federico II, Via Claudio 21, 80125 Naples, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
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2
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Fu Y, Zhao T, Clark F, Nomikou S, Tsirigos A, Lionnet T. Connecting Chromatin Structures to Gene Regulation Using Dynamic Polymer Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.07.566032. [PMID: 37986912 PMCID: PMC10659377 DOI: 10.1101/2023.11.07.566032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The transfer of regulatory information between distal loci on chromatin is thought to involve physical proximity, but key biophysical features of these contacts remain unclear. For instance, it is unknown how close and for how long two loci need to be in order to productively interact. The main challenge is that it is currently impossible to measure chromatin dynamics with high spatiotemporal resolution at scale. Polymer simulations provide an accessible and rigorous way to test biophysical models of chromatin regulation, yet there is a lack of simple and general methods for extracting the values of model parameters. Here we adapt the Nelder-Mead simplex optimization algorithm to select the best polymer model matching a given Hi-C dataset, using the MYC locus as an example. The model's biophysical parameters predict a compartmental rearrangement of the MYC locus in leukemia, which we validate with single-cell measurements. Leveraging trajectories predicted by the model, we find that loci with similar Hi-C contact frequencies can exhibit widely different contact dynamics. Interestingly, the frequency of productive interactions between loci exhibits a non-linear relationship with their Hi-C contact frequency when we enforce a specific capture radius and contact duration. These observations are consistent with recent experimental observations and suggest that the dynamic ensemble of chromatin configurations, rather than average contact matrices, is required to fully predict productive long-range chromatin interactions.
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3
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Pang QY, Chiu YC, Huang RYJ. Regulating epithelial-mesenchymal plasticity from 3D genome organization. Commun Biol 2024; 7:750. [PMID: 38902393 PMCID: PMC11190238 DOI: 10.1038/s42003-024-06441-w] [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: 09/26/2022] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a dynamic process enabling polarized epithelial cells to acquire mesenchymal features implicated in development and carcinoma progression. As our understanding evolves, it is clear the reversible execution of EMT arises from complex epigenomic regulation involving histone modifications and 3-dimensional (3D) genome structural changes, leading to a cascade of transcriptional events. This review summarizes current knowledge on chromatin organization in EMT, with a focus on hierarchical structures of the 3D genome and chromatin accessibility changes.
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Affiliation(s)
- Qing You Pang
- Neuro-Oncology Research Laboratory, National Neuroscience Institute, Singapore, 308433, Singapore
| | - Yi-Chia Chiu
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Ruby Yun-Ju Huang
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
- Center for Advanced Computing and Imaging in Biomedicine, National Taiwan University, Taipei, 10051, Taiwan.
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
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4
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Fouziya S, Krietenstein N, Mir US, Mieczkowski J, Khan MA, Baba A, Dar MA, Altaf M, Wani AH. Genome wide nucleosome landscape shapes 3D chromatin organization. SCIENCE ADVANCES 2024; 10:eadn2955. [PMID: 38848364 PMCID: PMC11160460 DOI: 10.1126/sciadv.adn2955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
The hierarchical chromatin organization begins with formation of nucleosomes, which fold into chromatin domains punctuated by boundaries and ultimately chromosomes. In a hierarchal organization, lower levels shape higher levels. However, the dependence of higher-order 3D chromatin organization on the nucleosome-level organization has not been studied in cells. We investigated the relationship between nucleosome-level organization and higher-order chromatin organization by perturbing nucleosomes across the genome by deleting Imitation SWItch (ISWI) and Chromodomain Helicase DNA-binding (CHD1) chromatin remodeling factors in budding yeast. We find that changes in nucleosome-level properties are accompanied by changes in 3D chromatin organization. Short-range chromatin contacts up to a few kilo-base pairs decrease, chromatin domains weaken, and boundary strength decreases. Boundary strength scales with accessibility and moderately with width of nucleosome-depleted region. Change in nucleosome positioning seems to alter the stiffness of chromatin, which can affect formation of chromatin contacts. Our results suggest a biomechanical "bottom-up" mechanism by which nucleosome distribution across genome shapes 3D chromatin organization.
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Affiliation(s)
- Shah Fouziya
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Nils Krietenstein
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | - Ulfat Syed Mir
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, J&K, 190006, India
| | - Jakub Mieczkowski
- International Research Agenda 3P Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
| | - Masood A. Khan
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Aemon Baba
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Mohmmad Abaas Dar
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Mohammad Altaf
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, J&K, 190006, India
| | - Ajazul H. Wani
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
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5
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Kabirova E, Ryzhkova A, Lukyanchikova V, Khabarova A, Korablev A, Shnaider T, Nuriddinov M, Belokopytova P, Smirnov A, Khotskin NV, Kontsevaya G, Serova I, Battulin N. TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene. Nat Commun 2024; 15:4521. [PMID: 38806452 PMCID: PMC11133455 DOI: 10.1038/s41467-024-48523-7] [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: 01/16/2023] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
Topologically associated domains (TADs) restrict promoter-enhancer interactions, thereby maintaining the spatiotemporal pattern of gene activity. However, rearrangements of the TADs boundaries do not always lead to significant changes in the activity pattern. Here, we investigated the consequences of the TAD boundaries deletion on the expression of developmentally important genes encoding tyrosine kinase receptors: Kit, Kdr, Pdgfra. We used genome editing in mice to delete the TADs boundaries at the Kit locus and characterized chromatin folding and gene expression in pure cultures of fibroblasts, mast cells, and melanocytes. We found that although Kit is highly active in both mast cells and melanocytes, deletion of the TAD boundary between the Kit and Kdr genes results in ectopic activation only in melanocytes. Thus, the epigenetic landscape, namely the mutual arrangement of enhancers and actively transcribing genes, is important for predicting the consequences of the TAD boundaries removal. We also found that mice without a TAD border between the Kit and Kdr genes have a phenotypic manifestation of the mutation - a lighter coloration. Thus, the data obtained shed light on the principles of interaction between the 3D chromatin organization and epigenetic marks in the regulation of gene activity.
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Affiliation(s)
- Evelyn Kabirova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | | | | | - Anna Khabarova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Alexey Korablev
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | | | | | - Polina Belokopytova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | | | | | - Irina Serova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
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6
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Li Y, Lee J, Bai L. DNA methylation-based high-resolution mapping of long-distance chromosomal interactions in nucleosome-depleted regions. Nat Commun 2024; 15:4358. [PMID: 38778058 PMCID: PMC11111806 DOI: 10.1038/s41467-024-48718-y] [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: 09/13/2023] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
3C-based methods have significantly advanced our understanding of 3D genome organization. However, it remains a formidable task to precisely capture long-range chromosomal interactions between individual loci, such as those between promoters and distal enhancers. Here, we present Methyltransferase Targeting-based chromosome Architecture Capture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome in budding yeast with high resolution and sensitivity. MTAC detects hundreds of intra- and inter-chromosomal interactions within nucleosome-depleted regions (NDRs) that cannot be captured by 4C, Hi-C, or Micro-C. By applying MTAC to various viewpoints, we find that (1) most long-distance chromosomal interactions detected by MTAC reflect tethering by the nuclear pore complexes (NPCs), (2) genes co-regulated by methionine assemble into inter-chromosomal clusters near NPCs upon activation, (3) mediated by condensin, the mating locus forms a highly specific interaction with the recombination enhancer (RE) in a mating-type specific manner, and (4) correlation of MTAC signals among NDRs reveal spatial mixing and segregation of the genome. Overall, these results demonstrate MTAC as a powerful tool to resolve fine-scale long-distance chromosomal interactions and provide insights into the 3D genome organization.
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Affiliation(s)
- Yi Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - James Lee
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA.
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7
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Samejima K, Gibcus JH, Abraham S, Cisneros-Soberanis F, Samejima I, Beckett AJ, Pučeková N, Abad MA, Medina-Pritchard B, Paulson JR, Xie L, Jeyaprakash AA, Prior IA, Mirny LA, Dekker J, Goloborodko A, Earnshaw WC. Rules of engagement for condensins and cohesins guide mitotic chromosome formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590027. [PMID: 38659940 PMCID: PMC11042376 DOI: 10.1101/2024.04.18.590027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
During mitosis, interphase chromatin is rapidly converted into rod-shaped mitotic chromosomes. Using Hi-C, imaging, proteomics and polymer modeling, we determine how the activity and interplay between loop-extruding SMC motors accomplishes this dramatic transition. Our work reveals rules of engagement for SMC complexes that are critical for allowing cells to refold interphase chromatin into mitotic chromosomes. We find that condensin disassembles interphase chromatin loop organization by evicting or displacing extrusive cohesin. In contrast, condensin bypasses cohesive cohesins, thereby maintaining sister chromatid cohesion while separating the sisters. Studies of mitotic chromosomes formed by cohesin, condensin II and condensin I alone or in combination allow us to develop new models of mitotic chromosome conformation. In these models, loops are consecutive and not overlapping, implying that condensins do not freely pass one another but stall upon encountering each other. The dynamics of Hi-C interactions and chromosome morphology reveal that during prophase loops are extruded in vivo at ~1-3 kb/sec by condensins as they form a disordered discontinuous helical scaffold within individual chromatids.
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Affiliation(s)
- Kumiko Samejima
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Johan H. Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
| | - Sameer Abraham
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology; Cambridge, USA
| | | | - Itaru Samejima
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Alison J. Beckett
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool; Liverpool, UK
| | - Nina Pučeková
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Maria Alba Abad
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Bethan Medina-Pritchard
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - James R. Paulson
- Department of Chemistry, University of Wisconsin-Oshkosh; Oshkosh, USA
| | - Linfeng Xie
- Department of Chemistry, University of Wisconsin-Oshkosh; Oshkosh, USA
| | - A. Arockia Jeyaprakash
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
- Gene Center Munich, Ludwig-Maximilians-Universität München; Munich, Germany
| | - Ian A. Prior
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool; Liverpool, UK
| | - Leonid A. Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology; Cambridge, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
| | | | - William C. Earnshaw
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
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8
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Hildebrand EM, Polovnikov K, Dekker B, Liu Y, Lafontaine DL, Fox AN, Li Y, Venev SV, Mirny LA, Dekker J. Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. Mol Cell 2024; 84:1422-1441.e14. [PMID: 38521067 DOI: 10.1016/j.molcel.2024.02.025] [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: 10/17/2022] [Revised: 10/23/2023] [Accepted: 02/24/2024] [Indexed: 03/25/2024]
Abstract
The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase chromosomes are largely free of entanglements. Here, we use Hi-C, polymer simulations, and multi-contact 3C and find that, by contrast, mitotic chromosomes are self-entangled. We explore how a mitotic self-entangled state is converted into an unentangled interphase state during mitotic exit. Most mitotic entanglements are removed during anaphase/telophase, with remaining ones removed during early G1, in a topoisomerase-II-dependent process. Polymer models suggest a two-stage disentanglement pathway: first, decondensation of mitotic chromosomes with remaining condensin loops produces entropic forces that bias topoisomerase II activity toward decatenation. At the second stage, the loops are released, and the formation of new entanglements is prevented by lower topoisomerase II activity, allowing the establishment of unentangled and territorial G1 chromosomes. When mitotic entanglements are not removed in experiments and models, a normal interphase state cannot be acquired.
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Affiliation(s)
- Erica M Hildebrand
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - Bastiaan Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Yu Liu
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Temple Health, Philadelphia, PA 19111, USA
| | - Denis L Lafontaine
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - A Nicole Fox
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ying Li
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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9
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Zou M, Lin A, Wang Y, Yang D, Liu X. The chromosome-level genome assembly of the giant dobsonfly Acanthacorydalis orientalis (McLachlan, 1899). Sci Data 2024; 11:351. [PMID: 38589366 PMCID: PMC11001986 DOI: 10.1038/s41597-024-03194-3] [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: 12/27/2023] [Accepted: 03/28/2024] [Indexed: 04/10/2024] Open
Abstract
Acanthacorydalis orientalis (McLachlan, 1899) (Megaloptera: Corydalidae) is an important freshwater-benthic invertebrate species that serves as an indicator for water-quality biomonitoring and is valuable for conservation from East Asia. Here, a high-quality reference genome for A. orientalis was constructed using Oxford Nanopore sequencing and High throughput Chromosome Conformation Capture (Hi-C) technology. The final genome size is 547.98 Mb, with the N50 values of contig and scaffold being 7.77 Mb and 50.53 Mb, respectively. The longest contig and scaffold are 20.57 Mb and 62.26 Mb in length, respectively. There are 99.75% contigs anchored onto 13 pseudo-chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis showed that the completeness of the genome assembly is 99.01%. There are 10,977 protein-coding genes identified, of which 84.00% are functionally annotated. The genome contains 44.86% repeat sequences. This high-quality genome provides substantial data for future studies on population genetics, aquatic adaptation, and evolution of Megaloptera and other related insect groups.
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Affiliation(s)
- Mingming Zou
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Aili Lin
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Yuyu Wang
- College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, China.
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10
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Yan AP, Salnikov PA, Gridina MM, Belokopytova PS, Fishman VS. Towards Development of the 4C-Based Method Detecting Interactions of Plasmid DNA with Host Genome. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:653-662. [PMID: 38831502 DOI: 10.1134/s0006297924040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/01/2024] [Accepted: 03/02/2024] [Indexed: 06/05/2024]
Abstract
Chromosome conformation capture techniques have revolutionized our understanding of chromatin architecture and dynamics at the genome-wide scale. In recent years, these methods have been applied to a diverse array of species, revealing fundamental principles of chromosomal organization. However, structural organization of the extrachromosomal entities, like viral genomes or plasmids, and their interactions with the host genome, remain relatively underexplored. In this work, we introduce an enhanced 4C-protocol tailored for probing plasmid DNA interactions. We design specific plasmid vector and optimize protocol to allow high detection rate of contacts between the plasmid and host DNA.
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Affiliation(s)
- Alexandra P Yan
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Paul A Salnikov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Maria M Gridina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Polina S Belokopytova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Veniamin S Fishman
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
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11
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Gridina MM, Stepanchuk YK, Nurridinov MA, Lagunov TA, Torgunakov NY, Shadsky AA, Ryabova AI, Vasiliev NV, Vtorushin SV, Gerashchenko TS, Denisov EV, Travin MA, Korolev MA, Fishman VS. Modification of the Hi-C Technology for Molecular Genetic Analysis of Formalin-Fixed Paraffin-Embedded Sections of Tumor Tissues. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:637-652. [PMID: 38831501 DOI: 10.1134/s0006297924040047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 06/05/2024]
Abstract
Molecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development; it is also necessary for the choice of targeted therapy. The Hi-C (high-throughput chromatin conformation capture) technology can be used to detect various types of genomic variants, including balanced chromosomal rearrangements, such as inversions and translocations. We propose a modification of the Hi-C method for the analysis of chromatin contacts in formalin-fixed paraffin-embedded (FFPE) sections of tumor tissues. The developed protocol allows to generate high-quality Hi-C data and detect all types of chromosomal rearrangements. We have analyzed various databases to compile a comprehensive list of translocations that hold clinical importance for the targeted therapy selection. The practical value of molecular genetic testing is its ability to influence the treatment strategies and to provide prognostic insights. Detecting specific chromosomal rearrangements can guide the choice of the targeted therapies, which is a critical aspect of personalized medicine in oncology.
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Affiliation(s)
- Maria M Gridina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yana K Stepanchuk
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Miroslav A Nurridinov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Timofey A Lagunov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Nikita Yu Torgunakov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Artem A Shadsky
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Anastasia I Ryabova
- Research Institute of Oncology, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - Nikolay V Vasiliev
- Research Institute of Oncology, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - Sergey V Vtorushin
- Research Institute of Oncology, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
- Siberian State Medical University, Ministry of Health of Russia, Tomsk, 634050, Russia
| | - Tatyana S Gerashchenko
- Research Institute of Oncology, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - Evgeny V Denisov
- Research Institute of Oncology, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - Mikhail A Travin
- Research Institute of Clinical and Experimental Lymphology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630117, Russia
| | - Maxim A Korolev
- Research Institute of Clinical and Experimental Lymphology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630117, Russia
| | - Veniamin S Fishman
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
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12
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Cheng G, Pratto F, Brick K, Li X, Alleva B, Huang M, Lam G, Camerini-Otero RD. High resolution maps of chromatin reorganization through mouse meiosis reveal novel features of the 3D meiotic structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586627. [PMID: 38903112 PMCID: PMC11188084 DOI: 10.1101/2024.03.25.586627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
When germ cells transition from the mitotic cycle into meiotic prophase I (MPI), chromosomes condense into an array of chromatin loops that are required to promote homolog pairing and genetic recombination. To identify the changes in chromosomal conformation, we isolated nuclei on a trajectory from spermatogonia to the end of MPI. At each stage along this trajectory, we built genomic interaction maps with the highest temporal and spatial resolution to date. The changes in chromatin folding coincided with a concurrent decline in mitotic cohesion and a rise in meiotic cohesin complexes. We found that the stereotypical large-scale A and B compartmentalization was lost during meiotic prophase I alongside the loss of topological associating domains (TADs). Still, local subcompartments were detected and maintained throughout meiosis. The enhanced Micro-C resolution revealed that, despite the loss of TADs, higher frequency contact sites between two loci were detectable during meiotic prophase I coinciding with CTCF bound sites. The pattern of interactions around these CTCF sites with their neighboring loci showed that CTCF sites were often anchoring the meiotic loops. Additionally, the localization of CTCF to the meiotic axes indicated that these anchors were at the base of loops. Strikingly, even in the face of the dramatic reconfiguration of interphase chromatin into a condensed loop-array, the interactions between regulatory elements remained well preserved. This establishes a potential mechanism for how the meiotic chromatin maintains active transcription within a highly structured genome. In summary, the high temporal and spatial resolution of these data revealed previously unappreciated aspects of mammalian meiotic chromatin organization.
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Affiliation(s)
- Gang Cheng
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Florencia Pratto
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Kevin Brick
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Xin Li
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin Alleva
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Mini Huang
- Present address: Sun Yat-Sen University, School of Medicine, Shen Zhen, China
| | - Gabriel Lam
- Present address: RNA Regulation Section, NIA, National Institutes of Health, Baltimore, MD, USA
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13
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Wall BPG, Nguyen M, Harrell JC, Dozmorov MG. Machine and deep learning methods for predicting 3D genome organization. ARXIV 2024:arXiv:2403.03231v1. [PMID: 38495565 PMCID: PMC10942493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.
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Affiliation(s)
- Brydon P. G. Wall
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - My Nguyen
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - J. Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Center for Pharmaceutical Engineering, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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14
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Liu T, Zhu Q, Kai Y, Bingham T, Wang S, Cha HJ, Mehta S, Schlaeger TM, Yuan GC, Orkin SH. Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions. Nat Commun 2024; 15:1274. [PMID: 38341433 PMCID: PMC10858947 DOI: 10.1038/s41467-024-45386-w] [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: 03/30/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Although emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood. Here we investigate the direct role of the abundant nuclear complex protein Matrin3 (Matr3) in chromatin architecture and development in the context of myogenesis. Using an acute targeted protein degradation platform (dTAG-Matr3), we reveal the dynamics of development-related chromatin reorganization. High-throughput chromosome conformation capture (Hi-C) experiments revealed substantial chromatin loop rearrangements soon after Matr3 depletion. Notably, YY1 binding was detected, accompanied by the emergence of novel YY1-mediated enhancer-promoter loops, which occurred concurrently with changes in histone modifications and chromatin-level binding patterns. Changes in chromatin occupancy by Matr3 also correlated with these alterations. Overall, our results suggest that Matr3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and highlight a conserved and direct role for Matr3 in maintenance of chromosomal architecture.
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Affiliation(s)
- Tianxin Liu
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Qian Zhu
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lester Sue Smith Breast Center, Department of Human Molecular Genetics, Baylor College of Medicine, 1 Moursund St, Houston, TX, 77030, USA
| | - Yan Kai
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Trevor Bingham
- Stem Cell Program, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Stacy Wang
- Lester Sue Smith Breast Center, Department of Human Molecular Genetics, Baylor College of Medicine, 1 Moursund St, Houston, TX, 77030, USA
| | - Hye Ji Cha
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical Science & Engineering, Dankook University, Cheonan, 31116, South Korea
| | - Stuti Mehta
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Guo-Cheng Yuan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stuart H Orkin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
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15
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Vinay ND, Singh K, Ellur RK, Chinnusamy V, Jaiswal S, Iquebal MA, Munshi AD, Matsumura H, Boopalakrishnan G, Jat GS, Kole C, Gaikwad AB, Kumar D, Dey SS, Behera TK. High-quality Momordica balsamina genome elucidates its potential use in improving stress resilience and therapeutic properties of bitter gourd. FRONTIERS IN PLANT SCIENCE 2024; 14:1258042. [PMID: 38333042 PMCID: PMC10851156 DOI: 10.3389/fpls.2023.1258042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 02/10/2024]
Abstract
Introduction Momordica balsamina is the closest wild species that can be crossed with an important fruit vegetable crop, Momordica charantia, has immense medicinal value, and placed under II subclass of primary gene pool of bitter gourd. M. balsamina is tolerant to major biotic and abiotic stresses. Genome characterization of Momordica balsamina as a wild relative of bitter gourd will contribute to the knowledge of the gene pool available for improvement in bitter gourd. There is potential to transfer gene/s related to biotic resistance and medicinal importance from M. balsamina to M. charantia to produce high-quality, better yielding and stress tolerant bitter gourd genotypes. Methods The present study provides the first and high-quality chromosome-level genome assembly of M. balsamina with size 384.90 Mb and N50 30.96 Mb using sequence data from 10x Genomics, Nanopore, and Hi-C platforms. Results A total of 6,32,098 transposons elements; 2,15,379 simple sequence repeats; 5,67,483 transcription factor binding sites; 3,376 noncoding RNA genes; and 41,652 protein-coding genes were identified, and 4,347 disease resistance, 67 heat stress-related, 05 carotenoid-related, 15 salt stress-related, 229 cucurbitacin-related, 19 terpenes-related, 37 antioxidant activity, and 06 sex determination-related genes were characterized. Conclusion Genome sequencing of M. balsamina will facilitate interspecific introgression of desirable traits. This information is cataloged in the form of webgenomic resource available at http://webtom.cabgrid.res.in/mbger/. Our finding of comparative genome analysis will be useful to get insights into the patterns and processes associated with genome evolution and to uncover functional regions of cucurbit genomes.
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Affiliation(s)
- N. D. Vinay
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Kalpana Singh
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ranjith Kumar Ellur
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anilabha Das Munshi
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | | | - G. Boopalakrishnan
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gograj Singh Jat
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | | | - Ambika Baladev Gaikwad
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shyam Sundar Dey
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Tusar Kanti Behera
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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16
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Sun L, Zhou J, Xu X, Liu Y, Ma N, Liu Y, Nie W, Zou L, Deng XW, He H. Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL. Nat Commun 2024; 15:35. [PMID: 38167349 PMCID: PMC10762229 DOI: 10.1038/s41467-023-44347-z] [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: 02/17/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.
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Affiliation(s)
- Linhua Sun
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Jingru Zhou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Xiao Xu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Yi Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Ni Ma
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
- PKU-Tsinghua-NIBS Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yutong Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Wenchao Nie
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, 430075, China
| | - Ling Zou
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, 430075, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China.
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China.
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.
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17
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Wilderman A, D'haene E, Baetens M, Yankee TN, Winchester EW, Glidden N, Roets E, Van Dorpe J, Janssens S, Miller DE, Galey M, Brown KM, Stottmann RW, Vergult S, Weaver KN, Brugmann SA, Cox TC, Cotney J. A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development. Nat Commun 2024; 15:136. [PMID: 38167838 PMCID: PMC10762089 DOI: 10.1038/s41467-023-44506-2] [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: 03/24/2022] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Craniofacial abnormalities account for approximately one third of birth defects. The regulatory programs that build the face require precisely controlled spatiotemporal gene expression, achieved through tissue-specific enhancers. Clusters of coactivated enhancers and their target genes, known as superenhancers, are important in determining cell identity but have been largely unexplored in development. In this study we identified superenhancer regions unique to human embryonic craniofacial tissue. To demonstrate the importance of such regions in craniofacial development and disease, we focused on an ~600 kb noncoding region located between NPVF and NFE2L3. We identified long range interactions with this region in both human and mouse embryonic craniofacial tissue with the anterior portion of the HOXA gene cluster. Mice lacking this superenhancer exhibit perinatal lethality, and present with highly penetrant skull defects and orofacial clefts phenocopying Hoxa2-/- mice. Moreover, we identified two cases of de novo copy number changes of the superenhancer in humans both with severe craniofacial abnormalities. This evidence suggests we have identified a critical noncoding locus control region that specifically regulates anterior HOXA genes and copy number changes are pathogenic in human patients.
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Affiliation(s)
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Machteld Baetens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Emma Wentworth Winchester
- Graduate Program UConn Health, Farmington, CT, USA
- University of Connecticut School of Dental Medicine, Farmington, CT, USA
| | - Nicole Glidden
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ellen Roets
- Department of Obstetrics, Women's Clinic, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute of Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Miranda Galey
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Kari M Brown
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Rolf W Stottmann
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - K Nicole Weaver
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Timothy C Cox
- Department of Oral & Craniofacial Sciences, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pediatrics, University of Missouri Kansas City, Kansas City, MO, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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18
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Lochs SJA, van der Weide RH, de Luca KL, Korthout T, van Beek RE, Kimura H, Kind J. Combinatorial single-cell profiling of major chromatin types with MAbID. Nat Methods 2024; 21:72-82. [PMID: 38049699 PMCID: PMC10776404 DOI: 10.1038/s41592-023-02090-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/17/2023] [Indexed: 12/06/2023]
Abstract
Gene expression programs result from the collective activity of numerous regulatory factors. Studying their cooperative mode of action is imperative to understand gene regulation, but simultaneously measuring these factors within one sample has been challenging. Here we introduce Multiplexing Antibodies by barcode Identification (MAbID), a method for combinatorial genomic profiling of histone modifications and chromatin-binding proteins. MAbID employs antibody-DNA conjugates to integrate barcodes at the genomic location of the epitope, enabling combined incubation of multiple antibodies to reveal the distributions of many epigenetic markers simultaneously. We used MAbID to profile major chromatin types and multiplexed measurements without loss of individual data quality. Moreover, we obtained joint measurements of six epitopes in single cells of mouse bone marrow and during mouse in vitro differentiation, capturing associated changes in multifactorial chromatin states. Thus, MAbID holds the potential to gain unique insights into the interplay between gene regulatory mechanisms, especially for low-input samples and in single cells.
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Affiliation(s)
- Silke J A Lochs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Robin H van der Weide
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Kim L de Luca
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Tessy Korthout
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ramada E van Beek
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Jop Kind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands.
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19
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Wright EM, Schalbetter S, Neale MJ. Hi-C2B: Optimized Detection of Chromosomal Contacts Within Synchronized Meiotic S. cerevisiae Cells. Methods Mol Biol 2024; 2818:45-63. [PMID: 39126466 DOI: 10.1007/978-1-0716-3906-1_3] [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] [Indexed: 08/12/2024]
Abstract
Hi-C, a genome-wide chromosome conformation capture assay, is a powerful tool used to study three-dimensional genome organization by converting physical pairwise interactions into counts of pairwise interactions. To study the many temporally regulated facets of meiotic recombination in S. cerevisiae, the Hi-C assay must be robust such that fine- and wide-scale comparisons between genetic datasets can be made. Here we describe an updated protocol for Hi-C (Hi-C2B) that generates reproducible libraries of interaction data with low noise and for a relatively low cost.
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Affiliation(s)
- Ellie M Wright
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | | | - Matthew J Neale
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK.
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20
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Sahu SK, Liu M, Wang G, Chen Y, Li R, Fang D, Sahu DN, Mu W, Wei J, Liu J, Zhao Y, Zhang S, Lisby M, Liu X, Xu X, Li L, Wang S, Liu H, He C. Chromosome-scale genomes of commercially important mahoganies, Swietenia macrophylla and Khaya senegalensis. Sci Data 2023; 10:832. [PMID: 38007506 PMCID: PMC10676371 DOI: 10.1038/s41597-023-02707-w] [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: 04/24/2023] [Accepted: 10/31/2023] [Indexed: 11/27/2023] Open
Abstract
Mahogany species (family Meliaceae) are highly valued for their aesthetic and durable wood. Despite their economic and ecological importance, genomic resources for mahogany species are limited, hindering genetic improvement and conservation efforts. Here we perform chromosome-scale genome assemblies of two commercially important mahogany species: Swietenia macrophylla and Khaya senegalensis. By combining 10X sequencing and Hi-C data, we assemble high-quality genomes of 274.49 Mb (S. macrophylla) and 406.50 Mb (K. senegalensis), with scaffold N50 lengths of 8.51 Mb and 7.85 Mb, respectively. A total of 99.38% and 98.05% of the assembled sequences are anchored to 28 pseudo-chromosomes in S. macrophylla and K. senegalensis, respectively. We predict 34,129 and 31,908 protein-coding genes in S. macrophylla and K. senegalensis, respectively, of which 97.44% and 98.49% are functionally annotated. The chromosome-scale genome assemblies of these mahogany species could serve as a vital genetic resource, especially in understanding the properties of non-model woody plants. These high-quality genomes could support the development of molecular markers for breeding programs, conservation efforts, and the sustainable management of these valuable forest resources.
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Affiliation(s)
- Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150400, China
| | - Guanlong Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- College of Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Ruirui Li
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, Chongqing Normal University, Chongqing, 400047, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Durgesh Nandini Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Weixue Mu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jinpu Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jie Liu
- Forestry Bureau of Ruili, Yunnan Dehong, Ruili, 678600, China
| | - Yuxian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Shouzhou Zhang
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518083, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150400, China.
| | - Chengzhong He
- Key Laboratory for Forest Genetic & Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China.
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21
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Liu Z, Huang Y, Chen H, Liu C, Wang M, Bian C, Wang L, Song L. Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat. BMC Genomics 2023; 24:679. [PMID: 37950158 PMCID: PMC10638732 DOI: 10.1186/s12864-023-09760-0] [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: 02/09/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The deep-sea snail Phymorhynchus buccinoides belongs to the genus Phymorhynchus (Neogastropoda: Raphitomidae), and it is a dominant specie in the cold seep habitat. As the environment of the cold seep is characterized by darkness, hypoxia and high concentrations of toxic substances such as hydrogen sulfide (H2S), exploration of the diverse fauna living around cold seeps will help to uncover the adaptive mechanisms to this unique habitat. In the present study, a chromosome-level genome of P. buccinoides was constructed and a series of genomic and transcriptomic analyses were conducted to explore its molecular adaptation mechanisms to the cold seep environments. RESULTS The assembled genome size of the P. buccinoides was approximately 2.1 Gb, which is larger than most of the reported snail genomes, possibly due to the high proportion of repetitive elements. About 92.0% of the assembled base pairs of contigs were anchored to 34 pseudo-chromosomes with a scaffold N50 size of 60.0 Mb. Compared with relative specie in the shallow water, the glutamate regulative and related genes were expanded in P. buccinoides, which contributes to the acclimation to hypoxia and coldness. Besides, the relatively high mRNA expression levels of the olfactory/chemosensory genes in osphradium indicate that P. buccinoides might have evolved a highly developed and sensitive olfactory organ for its orientation and predation. Moreover, the genome and transcriptome analyses demonstrate that P. buccinoides has evolved a sulfite-tolerance mechanism by performing H2S detoxification. Many genes involved in H2S detoxification were highly expressed in ctenidium and hepatopancreas, suggesting that these tissues might be critical for H2S detoxification and sulfite tolerance. CONCLUSIONS In summary, our report of this chromosome-level deep-sea snail genome provides a comprehensive genomic basis for the understanding of the adaptation strategy of P. buccinoides to the extreme environment at the deep-sea cold seeps.
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Affiliation(s)
- Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yuting Huang
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Chen
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Minxiao Wang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Bian
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
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22
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Alagna NS, Thomas TI, Wilson KL, Reddy KL. Choreography of lamina-associated domains: structure meets dynamics. FEBS Lett 2023; 597:2806-2822. [PMID: 37953467 PMCID: PMC10858991 DOI: 10.1002/1873-3468.14771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 11/14/2023]
Abstract
Lamina-associated domains are large regions of heterochromatin positioned at the nuclear periphery. These domains have been implicated in gene repression, especially in the context of development. In mammals, LAD organization is dependent on nuclear lamins, inner nuclear membrane proteins, and chromatin state. In addition, chromatin readers and modifier proteins have been implicated in this organization, potentially serving as molecular tethers that interact with both nuclear envelope proteins and chromatin. More recent studies have focused on teasing apart the rules that govern dynamic LAD organization and how LAD organization, in turn, relates to gene regulation and overall 3D genome organization. This review highlights recent studies in mammalian cells uncovering factors that instruct the choreography of LAD organization, re-organization, and dynamics at the nuclear lamina, including LAD dynamics in interphase and through mitotic exit, when LAD organization is re-established, as well as intra-LAD subdomain variations.
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Affiliation(s)
- Nicholas S. Alagna
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Tiera I. Thomas
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katherine L. Wilson
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Karen L. Reddy
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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23
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Wang Z, Liu Y, Wang H, Roy A, Liu H, Han F, Zhang X, Lu Q. Genome and transcriptome of Ips nitidus provide insights into high-altitude hypoxia adaptation and symbiosis. iScience 2023; 26:107793. [PMID: 37731610 PMCID: PMC10507238 DOI: 10.1016/j.isci.2023.107793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/15/2023] [Accepted: 08/29/2023] [Indexed: 09/22/2023] Open
Abstract
Ips nitidus is a well-known conifer pest that has contributed significantly to spruce forest disturbance in the Qinghai-Tibet Plateau and seriously threatens the ecological balance of these areas. We report a chromosome-level genome of I. nitidus determined by PacBio and Hi-C technology. Phylogenetic inference showed that it diverged from the common ancestor of I. typographus ∼2.27 mya. Gene family expansion in I. nitidus was characterized by DNA damage repair and energy metabolism, which may facilitate adaptation to high-altitude hypoxia. Interestingly, differential gene expression analysis revealed upregulated genes associated with high-altitude hypoxia adaptation and downregulated genes associated with detoxification after feeding and tunneling in fungal symbiont Ophiostoma bicolor-colonized substrates. Our findings provide evidence of the potential adaptability of I. nitidus to conifer host, high-altitude hypoxia and insight into how fungal symbiont assist in this process. This study enhances our understanding of insect adaptation, symbiosis, and pest management.
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Affiliation(s)
- Zheng Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
| | - Ya Liu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Huimin Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Amit Roy
- Faculty of Forestry and Wood Sciences, EXTEMIT-K and EVA.4.0 Unit, Czech University of Life Sciences, Kamýcká 1176, Prague 6, 165 00 Suchdol, Czech Republic
| | - Huixiang Liu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
| | | | - Xingyao Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Quan Lu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
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24
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Liu M, Wang W, Zhang H, Bi J, Zhang B, Shi T, Su G, Zheng Y, Fan S, Huang X, Chen B, Song Y, Zhao Z, Shi J, Li P, Lu W, Zhang L. Three-Dimensional Gene Regulation Network in Glioblastoma Ferroptosis. Int J Mol Sci 2023; 24:14945. [PMID: 37834393 PMCID: PMC10574000 DOI: 10.3390/ijms241914945] [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: 08/03/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Ferroptosis is an iron-dependent form of cell death, which is reported to be associated with glioma progression and drug sensitivity. Targeting ferroptosis is a potential therapeutic approach for glioma. However, the molecular mechanism of glioma cell ferroptosis is not clear. In this study, we profile the change of 3D chromatin structure in glioblastoma ferroptosis by using HiChIP and study the 3D gene regulation network in glioblastoma ferroptosis. A combination of an analysis of HiChIP and RNA-seq data suggests that change of chromatin loops mediated by 3D chromatin structure regulates gene expressions in glioblastoma ferroptosis. Genes that are regulated by 3D chromatin structures include genes that were reported to function in ferroptosis, like HDM2 and TXNRD1. We propose a new regulatory mechanism governing glioblastoma cell ferroptosis by 3D chromatin structure.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wange Lu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; (M.L.); (W.W.); (H.Z.); (J.B.); (B.Z.); (T.S.); (G.S.); (Y.Z.); (S.F.); (X.H.); (B.C.); (Y.S.); (Z.Z.); (J.S.); (P.L.)
| | - Lei Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; (M.L.); (W.W.); (H.Z.); (J.B.); (B.Z.); (T.S.); (G.S.); (Y.Z.); (S.F.); (X.H.); (B.C.); (Y.S.); (Z.Z.); (J.S.); (P.L.)
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25
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Guo S, Liu B, He J, Zhao Z, Zhang R, Li Z. Chromosome-level genome assembly of an important wolfberry fruit fly (Neoceratitis asiatica Becker). Sci Data 2023; 10:675. [PMID: 37794161 PMCID: PMC10551018 DOI: 10.1038/s41597-023-02601-5] [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: 05/22/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023] Open
Abstract
Tephritidae pests are significant agricultural pests with a notable impact on the economy, with a wide range of species and most having broad host ranges and strong reproductive abilities. However, the wolfberry fruit fly, Neoceratitis asiatica (Becker), is a Tephritidae fly which only harms wolfberry. Here, we assembled and annotated N. asiatica genome at the chromosome level and compared it with the genomic and transcriptomic information from other Tephritidae flies. The assembled genome of N. asiatica had a size of 563.8 Mb and achieved a completeness level of 99.1%, 18,387 genes were annotated totally. All contigs were assembled into 7 linkage groups with an N50 of 93.166 Mb assisted by the Hi-C technique. The high-quality genome developed here will provide a significant resource for exploring the genetic basis of the adaptive and reproductive differences among various Tephritidae pests, and provides an important theoretical basis for the prevention and control of Tephritidae pests.
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Affiliation(s)
- Shaokun Guo
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, P. R. China.
| | - Bo Liu
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, P. R. China
| | - Jia He
- Ningxia Key Laboratory of Plant Disease and Pest Control, Institute of Plant Protection, Academy of Ningxia Agriculture and Forestry Science, Yinchuan, Ningxia Hui Autonomous Region, P. R. China
| | - Zihua Zhao
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, P. R. China
| | - Rong Zhang
- Ningxia Key Laboratory of Plant Disease and Pest Control, Institute of Plant Protection, Academy of Ningxia Agriculture and Forestry Science, Yinchuan, Ningxia Hui Autonomous Region, P. R. China
| | - Zhihong Li
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, P. R. China.
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26
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Agarwal A, Korsak S, Choudhury A, Plewczynski D. The dynamic role of cohesin in maintaining human genome architecture. Bioessays 2023; 45:e2200240. [PMID: 37603403 DOI: 10.1002/bies.202200240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher-order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC-binding factor (CTCF) protein or other genome organizers. Cohesin plays a fundamental role in chromatin organization, gene expression and regulation. This review aims to describe the current understanding of the dynamic nature of the cohesin-DNA complex and its dependence on cohesin for genome maintenance. We discuss the current 3C technique and numerous bioinformatics pipelines used to comprehend structural genomics and epigenetics focusing on the analysis of Cohesin-centred interactions. We also incorporate our present comprehension of Loop Extrusion (LE) and insights from stochastic modelling.
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Affiliation(s)
- Abhishek Agarwal
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Sevastianos Korsak
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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27
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Lyu X, Xia Y, Wang C, Zhang K, Deng G, Shen Q, Gao W, Zhang M, Liao N, Ling J, Bo Y, Hu Z, Yang J, Zhang M. Pan-genome analysis sheds light on structural variation-based dissection of agronomic traits in melon crops. PLANT PHYSIOLOGY 2023; 193:1330-1348. [PMID: 37477947 DOI: 10.1093/plphys/kiad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023]
Abstract
Sweetness and appearance of fresh fruits are key palatable and preference attributes for consumers and are often controlled by multiple genes. However, fine-mapping the key loci or genes of interest by single genome-based genetic analysis is challenging. Herein, we present the chromosome-level genome assembly of 1 landrace melon accession (Cucumis melo ssp. agrestis) with wild morphologic features and thus construct a melon pan-genome atlas via integrating sequenced melon genome datasets. Our comparative genomic analysis reveals a total of 3.4 million genetic variations, of which the presence/absence variations (PAVs) are mainly involved in regulating the function of genes for sucrose metabolism during melon domestication and improvement. We further resolved several loci that are accountable for sucrose contents, flesh color, rind stripe, and suture using a structural variation (SV)-based genome-wide association study. Furthermore, via bulked segregation analysis (BSA)-seq and map-based cloning, we uncovered that a single gene, (CmPIRL6), determines the edible or inedible characteristics of melon fruit exocarp. These findings provide important melon pan-genome information and provide a powerful toolkit for future pan-genome-informed cultivar breeding of melon.
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Affiliation(s)
- Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuelin Xia
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenhao Wang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guancong Deng
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qinghui Shen
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wei Gao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
| | - Mengyi Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
| | - Nanqiao Liao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Yongming Bo
- Key Laboratory of Vegetable Breeding, Ningbo Weimeng Seed Co., Ltd, Ningbo 315100, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
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28
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Hung TH, So T, Thammavong B, Chamchumroon V, Theilade I, Phourin C, Bouamanivong S, Hartvig I, Gaisberger H, Jalonen R, Boshier DH, MacKay JJ. Range-wide differential adaptation and genomic offset in critically endangered Asian rosewoods. Proc Natl Acad Sci U S A 2023; 120:e2301603120. [PMID: 37549265 PMCID: PMC10438386 DOI: 10.1073/pnas.2301603120] [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: 01/29/2023] [Accepted: 06/15/2023] [Indexed: 08/09/2023] Open
Abstract
In the billion-dollar global illegal wildlife trade, rosewoods have been the world's most trafficked wild product since 2005. Dalbergia cochinchinensis and Dalbergia oliveri are the most sought-after rosewoods in the Greater Mekong Subregion. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts. Here, we present genome assemblies and range-wide genomic scans of adaptive variation, together with predictions of genomic offset to climate change. Adaptive genomic variation was differentially associated with temperature and precipitation-related variables between the species, although their natural ranges overlap. The findings are consistent with differences in pioneering ability and in drought tolerance. We predict their genomic offsets will increase over time and with increasing carbon emission pathway but at a faster pace in D. cochinchinensis than in D. oliveri. These results and the distinct gene-environment association in the eastern coastal edge of Vietnam suggest species-specific conservation actions: germplasm representation across the range in D. cochinchinensis and focused on hotspots of genomic offset in D. oliveri. We translated our genomic models into a seed source matching application, seedeR, to rapidly inform restoration efforts. Our ecological genomic research uncovering contrasting selection forces acting in sympatric rosewoods is of relevance to conserving tropical trees globally and combating risks from climate change.
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Affiliation(s)
- Tin Hang Hung
- Department of Biology, University of Oxford, OxfordOX1 3RB, United Kingdom
| | - Thea So
- Institute of Forest and Wildlife Research and Development, Phnom Penh, Cambodia
| | - Bansa Thammavong
- National Agriculture and Forestry Research Institute, Forestry Research Center, Vientiane, Laos
| | - Voradol Chamchumroon
- The Forest Herbarium, Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok10900, Thailand
| | - Ida Theilade
- Department of Food and Resource Economics, Faculty of Science, University of Copenhagen, Rolighedsvej 23, 1958Frederiksberg C, Denmark
| | - Chhang Phourin
- Institute of Forest and Wildlife Research and Development, Phnom Penh, Cambodia
| | - Somsanith Bouamanivong
- National Herbarium of Laos, Biotechnology and Ecology Institute, Ministry of Science and Technology, Vientiane, Laos
| | - Ida Hartvig
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958Frederiksberg C, Denmark
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
| | - Hannes Gaisberger
- Bioversity International, I-00057Rome, Italy
- Department of Geoinformatics, Paris Lodron University, 5020Salzburg, Austria
| | | | - David H. Boshier
- Department of Biology, University of Oxford, OxfordOX1 3RB, United Kingdom
| | - John J. MacKay
- Department of Biology, University of Oxford, OxfordOX1 3RB, United Kingdom
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29
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Senapati S, Irshad IU, Sharma AK, Kumar H. Fundamental insights into the correlation between chromosome configuration and transcription. Phys Biol 2023; 20:051002. [PMID: 37467757 DOI: 10.1088/1478-3975/ace8e5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression. In this article, we review the recent findings on three-dimensional interactions among chromosomes at the compartment, topologically associating domain, and loop levels and the impact of these interactions on the transcription process. We also discuss current understanding of various biophysical processes involved in multi-layer structural organization of chromosomes. Then, we discuss the relationships between gene expression and genome structure from perturbative genome-wide association studies. Furthermore, for a better understanding of how chromosome architecture and function are linked, we emphasize the role of epigenetic modifications in the regulation of gene expression. Such an understanding of the relationship between genome architecture and gene expression can provide a new perspective on the range of potential future discoveries and therapeutic research.
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Affiliation(s)
- Swayamshree Senapati
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
| | - Inayat Ullah Irshad
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
| | - Ajeet K Sharma
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, Jammu 181221, India
| | - Hemant Kumar
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
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30
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Patterson B, Yang B, Tanaka Y, Kim KY, Cakir B, Xiang Y, Kim J, Wang S, Park IH. Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. SCIENCE ADVANCES 2023; 9:eadf2245. [PMID: 37540754 PMCID: PMC10403202 DOI: 10.1126/sciadv.adf2245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 07/06/2023] [Indexed: 08/06/2023]
Abstract
Three-dimensional (3D) genomics shows immense promise for studying X chromosome inactivation (XCI) by interrogating changes to the X chromosomes' 3D states. Here, we sought to characterize the 3D state of the X chromosome in naïve and primed human pluripotent stem cells (hPSCs). Using chromatin tracing, we analyzed X chromosome folding conformations in these cells with megabase genomic resolution. X chromosomes in female naïve hPSCs exhibit folding conformations similar to the active X chromosome (Xa) and the inactive X chromosome (Xi) in somatic cells. However, naïve X chromosomes do not exhibit the chromatin compaction typically associated with these somatic X chromosome states. In H7 naïve human embryonic stem cells, XIST accumulation observed on damaged X chromosomes demonstrates the potential for naïve hPSCs to activate XCI-related mechanisms. Overall, our findings provide insight into the X chromosome status of naïve hPSCs with a single-chromosome resolution and are critical in understanding the unique epigenetic regulation in early embryonic cells.
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Affiliation(s)
- Benjamin Patterson
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bing Yang
- Department of Genetics, and Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bilal Cakir
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yangfei Xiang
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Siyuan Wang
- Department of Genetics, and Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
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Sahu SK, Liu M, Chen Y, Gui J, Fang D, Chen X, Yang T, He C, Cheng L, Yang J, Sahu DN, Li L, Wang H, Mu W, Wei J, Liu J, Zhao Y, Zhang S, Lisby M, Liu X, Xu X, Li L, Wang S, Liu H. Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis). Sci Data 2023; 10:512. [PMID: 37537171 PMCID: PMC10400565 DOI: 10.1038/s41597-023-02420-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
Wood is the most important natural and endlessly renewable source of energy. Despite the ecological and economic importance of wood, many aspects of its formation have not yet been investigated. We performed chromosome-scale genome assemblies of three timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis) which exhibit different wood properties such as wood density, hardness, growth rate, and fiber cell wall thickness. The combination of 10X, stLFR, Hi-Fi sequencing and HiC data led us to assemble high-quality genomes evident by scaffold N50 length of 55.97 Mb (O. pyramidale), 22.37 Mb (M. ferrea) and 14.55 Mb (T. grandis) with >97% BUSCO completeness of the assemblies. A total of 35774, 24027, and 44813 protein-coding genes were identified in M. ferrea, T. grandis and O. pyramidale, respectively. The data generated in this study is anticipated to serve as a valuable genetic resource and will promote comparative genomic analyses, and it is of practical importance in gaining a further understanding of the wood properties in non-model woody species.
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Affiliation(s)
- Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150400, China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jinshan Gui
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 311300, Hangzhou, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Xiaoli Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Ting Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Chengzhong He
- Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Le Cheng
- BGI Research, Kunming, Yunnan, 650106, China
| | - Jinlong Yang
- BGI Research, Kunming, Yunnan, 650106, China
- College of Forensic Science, Xi'an Jiaotong University, Xi'an, China
| | - Durgesh Nandini Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Weixue Mu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jinpu Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jie Liu
- Forestry Bureau of Ruili, Yunnan Dehong, Ruili, 678600, China
| | | | - Shouzhou Zhang
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150400, China.
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Han J, Wang S, Wu H, Zhao T, Guan X, Fang L. An upgraded method of high-throughput chromosome conformation capture (Hi-C 3.0) in cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1223591. [PMID: 37469786 PMCID: PMC10353440 DOI: 10.3389/fpls.2023.1223591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
High-throughput chromosome conformation capture (Hi-C) technology has been applied to explore the chromatin interactions and shed light on the biological functions of three-dimensional genomic features. However, it remains challenging to guarantee the high quality of Hi-C library in plants and hence the reliable capture of chromatin structures, especially loops, due to insufficient fragmentation and low efficiency of proximity ligations. To overcome these deficiencies, we optimized the parameters of the Hi-C protocol, principally the cross-linking agents and endonuclease fragmentation strategy. The double cross-linkers (FA+DSG) and double restriction enzymes (DpnII+DdeI) were utilized. Thus, a systematic in situ Hi-C protocol was designed using plant tissues embedded with comprehensive quality controls to monitor the library construction. This upgraded method, termed Hi-C 3.0, was applied to cotton leaves for trial. In comparison with the conventional Hi-C 2.0, Hi-C 3.0 can obtain more than 50% valid contacts at a given sequencing depth to improve the signal-to-noise ratio. Hi-C 3.0 can furthermore enhance the capturing of loops almost as twice as that of Hi-C 2.0. In addition, Hi-C 3.0 showed higher efficiency of compartment detection and identified compartmentalization more accurately. In general, Hi-C 3.0 contributes to the advancement of the Hi-C method in plants by promoting its capability on decoding the chromatin organization.
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Affiliation(s)
- Jin Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Siyuan Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hongyu Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
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Wang X, Zhao N, Cai L, Liu N, Zhu J, Yang B. High-quality chromosome-level scaffolds of the plant bug Pachypeltis micranthus provide insights into the availability of Mikania micrantha control. BMC Genomics 2023; 24:339. [PMID: 37340339 DOI: 10.1186/s12864-023-09445-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND The plant bug, Pachypeltis micranthus Mu et Liu (Hemiptera: Miridae), is an effective potential biological control agent for Mikania micrantha H.B.K. (Asteraceae; one of the most notorious invasive weeds worldwide). However, limited knowledge about this species hindered its practical application and research. Accordingly, sequencing the genome of this mirid bug holds great significance in controlling M. micrantha. RESULTS Here, 712.72 Mb high-quality chromosome-level scaffolds of P. micranthus were generated, of which 707.51 Mb (99.27%) of assembled sequences were anchored onto 15 chromosome-level scaffolds with contig N50 of 16.84 Mb. The P. micranthus genome had the highest GC content (42.43%) and the second highest proportion of repetitive sequences (375.82 Mb, 52.73%) than the three other mirid bugs (i.e., Apolygus lucorum, Cyrtorhinus lividipennis, and Nesidiocoris tenuis). Phylogenetic analysis showed that P. micranthus clustered with other mirid bugs and diverged from the common ancestor approximately 200 million years ago. Gene family expansion and/or contraction were analyzed, and significantly expanded gene families associated with P. micranthus feeding and adaptation to M. micrantha were manually identified. Compared with the whole body, transcriptome analysis of the salivary gland revealed that most of the upregulated genes were significantly associated with metabolism pathways and peptidase activity, particularly among cysteine peptidase, serine peptidase, and polygalacturonase; this could be one of the reasons for precisely and highly efficient feeding by the oligophagous bug P. micranthus on M. micrantha. CONCLUSION Collectively, this work provides a crucial chromosome-level scaffolds resource to study the evolutionary adaptation between mirid bug and their host. It is also helpful in searching for novel environment-friendly biological strategies to control M. micrantha.
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Affiliation(s)
- Xiafei Wang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Ning Zhao
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Liqiong Cai
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Naiyong Liu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jiaying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Bin Yang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China.
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Jia SL, Zhang M, Liu GL, Chi ZM, Chi Z. Novel chromosomes and genomes provide new insights into evolution and adaptation of the whole genome duplicated yeast-like fungus TN3-1 isolated from natural honey. Funct Integr Genomics 2023; 23:206. [PMID: 37335429 DOI: 10.1007/s10142-023-01127-8] [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: 04/20/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
Aureobasidium melanogenum TN3-1 strain and A. melanogenum P16 strain were isolated from the natural honey and the mangrove ecosystem, respectively. The former can produce much higher pullulan from high concentration of glucose than the latter. In order to know what happened to their genomes, the PacBio sequencing and Hi-C technologies were used to create the first high-quality chromosome-level reference genome assembly of A. melanogenum TN3-1 (51.61 Mb) and A. melanogenum P16 (25.82 Mb) with the contig N50 of 2.19 Mb and 2.26 Mb, respectively. Based on the Hi-C results, a total of 93.33% contigs in the TN3-1 strain and 92.31% contigs in the P16 strain were anchored onto 24 and 12 haploid chromosomes, respectively. The genomes of the TN3-1 strain had two subgenomes A and B. Synteny analysis showed that the genomic contents of the two subgenomes were asymmetric with many structural variations. Intriguingly, the TN3-1 strain was revealed as a recent hybrid/fusion between the ancestor of A. melanogenum CBS105.22/CBS110374 and the ancestor of another unidentified strain of A. melanogenum similar to P16 strain. We estimated that the two ancient progenitors diverged around 18.38 Mya and merged around 10.66-9.98 Mya. It was found that in the TN3-1 strain, telomeres of each chromosome contained high level of long interspersed nuclear elements (LINEs), but had low level of the telomerase encoding gene. Meanwhile, there were high level of transposable elements (TEs) inserted in the chromosomes of the TN3-1 strain. In addition, the positively selected genes of the TN3-1 strain were mainly enriched in the metabolic processes related to harsh environmental adaptability. Most of the stress-related genes were found to be related to the adjacent LTRs, and the glucose derepression was caused by the mutation of the Glc7-2 in the Snf-Mig1 system. All of these could contribute to its genetic instability, genome evolution, high stress resistance, and high pullulan production from glucose.
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Affiliation(s)
- Shu-Lei Jia
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China
| | - Mei Zhang
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China
| | - Guang-Lei Liu
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Zhen-Ming Chi
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.
| | - Zhe Chi
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
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Syed SA, Shqillo K, Nand A, Zhan Y, Dekker J, Imbalzano AN. Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544859. [PMID: 37398486 PMCID: PMC10312757 DOI: 10.1101/2023.06.13.544859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Protein arginine methyltransferase 5 (Prmt5) is an essential regulator of embryonic development and adult progenitor cell functions. Prmt5 expression is mis-regulated in many cancers, and the development of Prmt5 inhibitors as cancer therapeutics is an active area of research. Prmt5 functions via effects on gene expression, splicing, DNA repair, and other critical cellular processes. We examined whether Prmt5 functions broadly as a genome-wide regulator of gene transcription and higher-order chromatin interactions during the initial stages of adipogenesis using ChIP-Seq, RNA-seq, and Hi-C using 3T3-L1 cells, a frequently utilized model for adipogenesis. We observed robust genome-wide Prmt5 chromatin-binding at the onset of differentiation. Prmt5 localized to transcriptionally active genomic regions, acting as both a positive and a negative regulator. A subset of Prmt5 binding sites co-localized with mediators of chromatin organization at chromatin loop anchors. Prmt5 knockdown decreased insulation strength at the boundaries of topologically associating domains (TADs) adjacent to sites with Prmt5 and CTCF co-localization. Genes overlapping such weakened TAD boundaries showed transcriptional dysregulation. This study identifies Prmt5 as a broad regulator of gene expression, including regulation of early adipogenic factors, and reveals an unappreciated requirement for Prmt5 in maintaining strong insulation at TAD boundaries and overall chromatin organization.
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Affiliation(s)
- Sabriya A Syed
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Kristina Shqillo
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Ankita Nand
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Ye Zhan
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Job Dekker
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
- Howard Hughes Medical Institute, Chevy Chase, MD USA
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
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Boyd RJ, McClymont SA, Barrientos NB, Hook PW, Law WD, Rose RJ, Waite EL, Rathinavelu J, Avramopoulos D, McCallion AS. Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons. BMC Genomics 2023; 24:306. [PMID: 37286935 PMCID: PMC10245633 DOI: 10.1186/s12864-023-09398-y] [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: 01/27/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023] Open
Abstract
To overcome the ethical and technical limitations of in vivo human disease models, the broader scientific community frequently employs model organism-derived cell lines to investigate disease mechanisms, pathways, and therapeutic strategies. Despite the widespread use of certain in vitro models, many still lack contemporary genomic analysis supporting their use as a proxy for the affected human cells and tissues. Consequently, it is imperative to determine how accurately and effectively any proposed biological surrogate may reflect the biological processes it is assumed to model. One such cellular surrogate of human disease is the established mouse neural precursor cell line, SN4741, which has been used to elucidate mechanisms of neurotoxicity in Parkinson disease for over 25 years. Here, we are using a combination of classic and contemporary genomic techniques - karyotyping, RT-qPCR, single cell RNA-seq, bulk RNA-seq, and ATAC-seq - to characterize the transcriptional landscape, chromatin landscape, and genomic architecture of this cell line, and evaluate its suitability as a proxy for midbrain dopaminergic neurons in the study of Parkinson disease. We find that SN4741 cells possess an unstable triploidy and consistently exhibits low expression of dopaminergic neuron markers across assays, even when the cell line is shifted to the non-permissive temperature that drives differentiation. The transcriptional signatures of SN4741 cells suggest that they are maintained in an undifferentiated state at the permissive temperature and differentiate into immature neurons at the non-permissive temperature; however, they may not be dopaminergic neuron precursors, as previously suggested. Additionally, the chromatin landscapes of SN4741 cells, in both the differentiated and undifferentiated states, are not concordant with the open chromatin profiles of ex vivo, mouse E15.5 forebrain- or midbrain-derived dopaminergic neurons. Overall, our data suggest that SN4741 cells may reflect early aspects of neuronal differentiation but are likely not a suitable proxy for dopaminergic neurons as previously thought. The implications of this study extend broadly, illuminating the need for robust biological and genomic rationale underpinning the use of in vitro models of molecular processes.
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Affiliation(s)
- Rachel J. Boyd
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Sarah A. McClymont
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Nelson B. Barrientos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Paul W. Hook
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - William D. Law
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Rebecca J. Rose
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Eric L. Waite
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Jay Rathinavelu
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Dimitrios Avramopoulos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Andrew S. McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
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Zhang Z, Xia T, Zhou S, Yang X, Lyu T, Wang L, Fang J, Wang Q, Dou H, Zhang H. High-Quality Chromosome-Level Genome Assembly of the Corsac Fox ( Vulpes corsac) Reveals Adaptation to Semiarid and Harsh Environments. Int J Mol Sci 2023; 24:ijms24119599. [PMID: 37298549 DOI: 10.3390/ijms24119599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
The Corsac fox (Vulpes corsac) is a species of fox distributed in the arid prairie regions of Central and Northern Asia, with distinct adaptations to dry environments. Here, we applied Oxford-Nanopore sequencing and a chromosome structure capture technique to assemble the first Corsac fox genome, which was then assembled into chromosome fragments. The genome assembly has a total length of 2.2 Gb with a contig N50 of 41.62 Mb and a scaffold N50 of 132.2 Mb over 18 pseudo-chromosomal scaffolds. The genome contained approximately 32.67% of repeat sequences. A total of 20,511 protein-coding genes were predicted, of which 88.9% were functionally annotated. Phylogenetic analyses indicated a close relation to the Red fox (Vulpes vulpes) with an estimated divergence time of ~3.7 million years ago (MYA). We performed separate enrichment analyses of species-unique genes, the expanded and contracted gene families, and positively selected genes. The results suggest an enrichment of pathways related to protein synthesis and response and an evolutionary mechanism by which cells respond to protein denaturation in response to heat stress. The enrichment of pathways related to lipid and glucose metabolism, potentially preventing stress from dehydration, and positive selection of genes related to vision, as well as stress responses in harsh environments, may reveal adaptive evolutionary mechanisms in the Corsac fox under harsh drought conditions. Additional detection of positive selection for genes associated with gustatory receptors may reveal a unique desert diet strategy for the species. This high-quality genome provides a valuable resource for studying mammalian drought adaptation and evolution in the genus Vulpes.
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Affiliation(s)
- Zhihao Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tian Xia
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Xiufeng Yang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tianshu Lyu
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lidong Wang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Jiaohui Fang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Honghai Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
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Zhang X, Yu G, Dai Y, Zhang H, Wang K, Han J. High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon. BMC PLANT BIOLOGY 2023; 23:260. [PMID: 37193952 DOI: 10.1186/s12870-023-04269-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/06/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND The adaptation of plants to cold stress involves changes in gene expression profiles that are associated with epigenetic regulation. Although the three-dimensional (3D) genome architecture is considered an important epigenetic regulator, the role of 3D genome organization in the cold stress response remains unclear. RESULTS In this study, we developed high-resolution 3D genomic maps using control and cold-treated leaf tissue of the model plant Brachypodium distachyon using Hi-C to determine how cold stress affects the 3D genome architecture. We generated ~ 1.5 kb resolution chromatin interaction maps and showed that cold stress disrupts different levels of chromosome organization, including A/B compartment transition, a reduction in chromatin compartmentalization and the size of topologically associating domains (TADs), and loss of long-range chromatin loops. Integrating RNA-seq information, we identified cold-response genes and revealed that transcription was largely unaffected by the A/B compartment transition. The cold-response genes were predominantly localized in compartment A. In contrast, transcriptional changes are required for TAD reorganization. We demonstrated that dynamic TAD events were associated with H3K27me3 and H3K27ac state alterations. Moreover, a loss of chromatin looping, rather than a gain of looping, coincides with alterations in gene expression, indicating that chromatin loop disruption may play a more important role than loop formation in the cold-stress response. CONCLUSIONS Our study highlights the multiscale 3D genome reprogramming that occurs during cold stress and expands our knowledge of the mechanisms underlying transcriptional regulation in response to cold stress in plants.
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Affiliation(s)
- Xin Zhang
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Guangrun Yu
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Yan Dai
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Hui Zhang
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, 226019, China.
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, 226019, China.
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Zhou CY, Dekker B, Liu Z, Cabrera H, Ryan J, Dekker J, Heald R. Mitotic chromosomes scale to nuclear-cytoplasmic ratio and cell size in Xenopus. eLife 2023; 12:e84360. [PMID: 37096661 PMCID: PMC10260010 DOI: 10.7554/elife.84360] [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: 10/21/2022] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
During the rapid and reductive cleavage divisions of early embryogenesis, subcellular structures such as the nucleus and mitotic spindle scale to decreasing cell size. Mitotic chromosomes also decrease in size during development, presumably to scale coordinately with mitotic spindles, but the underlying mechanisms are unclear. Here we combine in vivo and in vitro approaches using eggs and embryos from the frog Xenopus laevis to show that mitotic chromosome scaling is mechanistically distinct from other forms of subcellular scaling. We found that mitotic chromosomes scale continuously with cell, spindle, and nuclear size in vivo. However, unlike for spindles and nuclei, mitotic chromosome size cannot be reset by cytoplasmic factors from earlier developmental stages. In vitro, increasing nuclear-cytoplasmic (N/C) ratio is sufficient to recapitulate mitotic chromosome scaling, but not nuclear or spindle scaling, through differential loading of maternal factors during interphase. An additional pathway involving importin α scales mitotic chromosomes to cell surface area/volume ratio (SA/V) during metaphase. Finally, single-chromosome immunofluorescence and Hi-C data suggest that mitotic chromosomes shrink during embryogenesis through decreased recruitment of condensin I, resulting in major rearrangements of DNA loop architecture to accommodate the same amount of DNA on a shorter chromosome axis. Together, our findings demonstrate how mitotic chromosome size is set by spatially and temporally distinct developmental cues in the early embryo.
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Affiliation(s)
- Coral Y Zhou
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Bastiaan Dekker
- Department of Systems Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Ziyuan Liu
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Hilda Cabrera
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Joel Ryan
- Advanced BioImaging Facility, McGill UniversityMontrealCanada
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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Wang B, Ji L, Bian Q. SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites. Cell Rep 2023; 42:112323. [PMID: 37000624 DOI: 10.1016/j.celrep.2023.112323] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/20/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023] Open
Abstract
Special AT-rich sequence binding protein 1 (SATB1) has long been proposed to act as a global chromatin loop organizer in T cells. However, the exact functions of SATB1 in spatial genome organization remain elusive. Here we show that the depletion of SATB1 in human and murine T cells leads to transcriptional dysregulation for genes involved in T cell activation, as well as alterations of 3D genome architecture at multiple levels, including compartments, topologically associating domains, and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 leads to increased chromatin contacts among and across the SATB1/CTCF co-occupied sites, thereby affecting the transcription of critical regulators of T cell activation. The loss of SATB1 does not affect CTCF occupancy but significantly reduces the retention of CTCF in the nuclear matrix. Collectively, our data show that SATB1 contributes to 3D genome organization by constraining chromatin topology surrounding CTCF-binding sites.
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Affiliation(s)
- Bao Wang
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Luzhang Ji
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Qian Bian
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China; Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Zhang Z, Pei P, Zhang M, Li F, Tang G. Chromosome-level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure. PEST MANAGEMENT SCIENCE 2023; 79:1467-1482. [PMID: 36502364 DOI: 10.1002/ps.7319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 10/26/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Dastarcus helophoroides is an important natural enemy of cerambycids, and is wildly used in biological control of pests. Nevertheless, the absence of complete genomic information limits the investigation of the underlying molecular mechanisms. Here, a chromosome-level of Dastarcus helophoroides genome is assembled using a combination strategy of Illumina, PacBio, 10x™ Genomics, and Hi-C. RESULTS The final assembly is 609.09 Mb with contig N50, scaffold N50 and GC content of 5.46 Mb, 42.56 Mb and 31.50%, respectively, and 95.25% of the contigs anchor into 13 chromosomes. In total 14 890 protein-coding genes and 65.37% repeat sequences are predicted in the assembly genome. The phylogenetic analysis of single-copy gene families shared among 20 insect species indicates that Dastarcus helophoroides is placed as the sister species to clade (Nitidulidae+Curculionoidea+Chrysomeloidea) + Tenebrionoidea, and diverges from the related species ~242.9 Mya. In total 36 expanded gene families are identified in Dastarcus helophoroides genome, and are functionally related to drug metabolism and metabolism of xenobiotics by cytochrome P450. Some members of CYP4 Clade and CYP6 Clade are up-regulated in Dastarcus helophoroides adults upon insecticide exposure, of which expressions of DhCYP4Q, DhCYP6A14X1 and DhCYP4C1 are significantly up-regulated. The silencing of the three genes leads to adults more sensitive to insecticide and increased knocked-down rate, which may indicate their critical roles in stress resistance and detoxication. CONCLUSION Our study systematically integrated the chromosome-level genome, transcriptome and gene expression of Dastarcus helophoroides, which will provide valuable resources for understanding mechanisms of pesticide metabolism, growth and development, and utilization of the natural enemy in integrated control. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Zhengqing Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Pei Pei
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Feifei Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
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Marlétaz F, de la Calle-Mustienes E, Acemel RD, Paliou C, Naranjo S, Martínez-García PM, Cases I, Sleight VA, Hirschberger C, Marcet-Houben M, Navon D, Andrescavage A, Skvortsova K, Duckett PE, González-Rajal Á, Bogdanovic O, Gibcus JH, Yang L, Gallardo-Fuentes L, Sospedra I, Lopez-Rios J, Darbellay F, Visel A, Dekker J, Shubin N, Gabaldón T, Nakamura T, Tena JJ, Lupiáñez DG, Rokhsar DS, Gómez-Skarmeta JL. The little skate genome and the evolutionary emergence of wing-like fins. Nature 2023; 616:495-503. [PMID: 37046085 PMCID: PMC10115646 DOI: 10.1038/s41586-023-05868-1] [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: 03/23/2022] [Accepted: 02/21/2023] [Indexed: 04/14/2023]
Abstract
Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins-including gene expression, chromatin occupancy and three-dimensional conformation-we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.
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Affiliation(s)
- Ferdinand Marlétaz
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan.
| | - Elisa de la Calle-Mustienes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
- Epigenetics and Sex Development Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Christina Paliou
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Ildefonso Cases
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Victoria A Sleight
- Department of Zoology, University of Cambridge, Cambridge, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BCS-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dina Navon
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA
| | - Ali Andrescavage
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA
| | - Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Paul Edward Duckett
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Álvaro González-Rajal
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Johan H Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Liyan Yang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Lourdes Gallardo-Fuentes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Ismael Sospedra
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Fabrice Darbellay
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
- School of Natural Sciences, University of California, Merced, CA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Neil Shubin
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Tetsuya Nakamura
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA.
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain.
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
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Chen M, Liu X, Liu Q, Shi D, Li H. 3D genomics and its applications in precision medicine. Cell Mol Biol Lett 2023; 28:19. [PMID: 36879202 PMCID: PMC9987123 DOI: 10.1186/s11658-023-00428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/06/2023] [Indexed: 03/08/2023] Open
Abstract
Three-dimensional (3D) genomics is an emerging discipline that studies the three-dimensional structure of chromatin and the three-dimensional and functions of genomes. It mainly studies the three-dimensional conformation and functional regulation of intranuclear genomes, such as DNA replication, DNA recombination, genome folding, gene expression regulation, transcription factor regulation mechanism, and the maintenance of three-dimensional conformation of genomes. Self-chromosomal conformation capture (3C) technology has been developed, and 3D genomics and related fields have developed rapidly. In addition, chromatin interaction analysis techniques developed by 3C technologies, such as paired-end tag sequencing (ChIA-PET) and whole-genome chromosome conformation capture (Hi-C), enable scientists to further study the relationship between chromatin conformation and gene regulation in different species. Thus, the spatial conformation of plant, animal, and microbial genomes, transcriptional regulation mechanisms, interaction patterns of chromosomes, and the formation mechanism of spatiotemporal specificity of genomes are revealed. With the help of new experimental technologies, the identification of key genes and signal pathways related to life activities and diseases is sustaining the rapid development of life science, agriculture, and medicine. In this paper, the concept and development of 3D genomics and its application in agricultural science, life science, and medicine are introduced, which provides a theoretical basis for the study of biological life processes.
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Affiliation(s)
- Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China
| | - Xingyu Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China.,Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China.
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China.
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Lopdell TJ. Using QTL to Identify Genes and Pathways Underlying the Regulation and Production of Milk Components in Cattle. Animals (Basel) 2023; 13:ani13050911. [PMID: 36899768 PMCID: PMC10000085 DOI: 10.3390/ani13050911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Milk is a complex liquid, and the concentrations of many of its components are under genetic control. Many genes and pathways are known to regulate milk composition, and the purpose of this review is to highlight how the discoveries of quantitative trait loci (QTL) for milk phenotypes can elucidate these pathways. The main body of this review focuses primarily on QTL discovered in cattle (Bos taurus) as a model species for the biology of lactation, and there are occasional references to sheep genetics. The following section describes a range of techniques that can be used to help identify the causative genes underlying QTL when the underlying mechanism involves the regulation of gene expression. As genotype and phenotype databases continue to grow and diversify, new QTL will continue to be discovered, and although proving the causality of underlying genes and variants remains difficult, these new data sets will further enhance our understanding of the biology of lactation.
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Gridina MM, Vesna E, Minzhenkova ME, Shilova NV, Ryzhkova OP, Nazarenko LP, Belyaeva EO, Lebedev IN, Fishman VS. Influence of human peripheral blood samples preprocessing on the quality of Hi-C libraries. Vavilovskii Zhurnal Genet Selektsii 2023; 27:83-87. [PMID: 36923477 PMCID: PMC10009481 DOI: 10.18699/vjgb-23-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 03/18/2023] Open
Abstract
The genome-wide variant of the chromatin conformation capture technique (Hi-C) is a powerful tool for revealing patterns of genome spatial organization, as well as for understanding the effects of their disturbance on disease development. In addition, Hi-C can be used to detect chromosomal rearrangements, including balanced translocations and inversions. The use of the Hi-C method for the detection of chromosomal rearrangements is becoming more widespread. Modern high-throughput methods of genome analysis can effectively reveal point mutations and unbalanced chromosomal rearrangements. However, their sensitivity for determining translocations and inversions remains rather low. The storage of whole blood samples can affect the amount and integrity of genomic DNA, and it can distort the results of subsequent analyses if the storage was not under proper conditions. The Hi-C method is extremely demanding on the input material. The necessary condition for successfully applying Hi-C and obtaining high-quality data is the preservation of the spatial chromatin organization within the nucleus. The purpose of this study was to determine the optimal storage conditions of blood samples for subsequent Hi-C analysis. We selected 10 different conditions for blood storage and sample processing. For each condition, we prepared and sequenced Hi-C libraries. The quality of the obtained data was compared. As a result of the work, we formulated the requirements for the storage and processing of samples to obtain high-quality Hi-C data. We have established the minimum volume of blood sufficient for conducting Hi-C analysis. In addition, we have identified the most suitable methods for isolation of peripheral blood mononuclear cells and their long-term storage. The main requirement we have formulated is not to freeze whole blood.
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Affiliation(s)
- M M Gridina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E Vesna
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - N V Shilova
- Research Centre for Medical Genetics, Moscow, Russia
| | - O P Ryzhkova
- Research Centre for Medical Genetics, Moscow, Russia
| | - L P Nazarenko
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - E O Belyaeva
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I N Lebedev
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - V S Fishman
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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46
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Khabarova A, Koksharova G, Salnikov P, Belokopytova P, Mungalov R, Pristyazhnuk I, Nurislamov A, Gridina M, Fishman V. A Cre-LoxP-based approach for combinatorial chromosome rearrangements in human HAP1 cells. Chromosome Res 2023; 31:11. [PMID: 36842155 DOI: 10.1007/s10577-023-09719-7] [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: 12/15/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/27/2023]
Abstract
Alterations of human karyotype caused by chromosomal rearrangements are often associated with considerable phenotypic effects. Studying molecular mechanisms underlying these effects requires an efficient and scalable experimental model. Here, we propose a Cre-LoxP-based approach for the generation of combinatorial diversity of chromosomal rearrangements. We demonstrate that using the developed system, both intra- and inter-chromosomal rearrangements can be induced in the human haploid HAP1 cells, although the latter is significantly less effective. The obtained genetically modified HAP1 cell line can be used to dissect genomic effects associated with intra-chromosomal structural variations.
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Affiliation(s)
| | - Galina Koksharova
- Institute of Cytology and Genetics, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | - Pavel Salnikov
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Polina Belokopytova
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | | | - Artem Nurislamov
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Maria Gridina
- Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- Artificial Intelligence Research Institute, AIRI, Moscow, Russia
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Boyd RJ, McClymont SA, Barrientos NB, Hook PW, Law WD, Rose RJ, Waite EL, Rathinavelu J, Avramopoulos D, McCallion AS. Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons. RESEARCH SQUARE 2023:rs.3.rs-2520557. [PMID: 36824793 PMCID: PMC9949168 DOI: 10.21203/rs.3.rs-2520557/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
To overcome the ethical and technical limitations of in vivo human disease models, the broader scientific community frequently employs model organism-derived cell lines to investigate of disease mechanisms, pathways, and therapeutic strategies. Despite the widespread use of certain in vitro models, many still lack contemporary genomic analysis supporting their use as a proxy for the affected human cells and tissues. Consequently, it is imperative to determine how accurately and effectively any proposed biological surrogate may reflect the biological processes it is assumed to model. One such cellular surrogate of human disease is the established mouse neural precursor cell line, SN4741, which has been used to elucidate mechanisms of neurotoxicity in Parkinson disease for over 25 years. Here, we are using a combination of classic and contemporary genomic techniques - karyotyping, RT-qPCR, single cell RNA-seq, bulk RNA-seq, and ATAC-seq - to characterize the transcriptional landscape, chromatin landscape, and genomic architecture of this cell line, and evaluate its suitability as a proxy for midbrain dopaminergic neurons in the study of Parkinson disease. We find that SN4741 cells possess an unstable triploidy and consistently exhibits low expression of dopaminergic neuron markers across assays, even when the cell line is shifted to the non-permissive temperature that drives differentiation. The transcriptional signatures of SN4741 cells suggest that they are maintained in an undifferentiated state at the permissive temperature and differentiate into immature neurons at the non-permissive temperature; however, they may not be dopaminergic neuron precursors, as previously suggested. Additionally, the chromatin landscapes of SN4741 cells, in both the differentiated and undifferentiated states, are not concordant with the open chromatin profiles of ex vivo , mouse E15.5 forebrain- or midbrain-derived dopaminergic neurons. Overall, our data suggest that SN4741 cells may reflect early aspects of neuronal differentiation but are likely not a suitable a proxy for dopaminergic neurons as previously thought. The implications of this study extend broadly, illuminating the need for robust biological and genomic rationale underpinning the use of in vitro models of molecular processes.
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Maslova A, Plotnikov V, Nuriddinov M, Gridina M, Fishman V, Krasikova A. Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line. BMC Genomics 2023; 24:66. [PMID: 36750787 PMCID: PMC9906895 DOI: 10.1186/s12864-023-09158-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Karyotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal rearrangements can cause dramatic changes in gene expression and affect cellular phenotype and behavior during in vitro culture. Structural variations of chromosomes in many continuous mammalian cell lines are well documented, but chromosome aberrations in cell lines from other vertebrate models often remain understudied. The chicken LSCC-HD3 cell line (HD3), generated from erythroid precursors, was used as an avian model for erythroid differentiation and lineage-specific gene expression. However, karyotype abnormalities in the HD3 cell line were not assessed. In the present study, we applied high-throughput chromosome conformation capture to analyze 3D genome organization and to detect chromosome rearrangements in the HD3 cell line. RESULTS We obtained Hi-C maps of genomic interactions for the HD3 cell line and compared A/B compartments and topologically associating domains between HD3 and several other cell types. By analysis of contact patterns in the Hi-C maps of HD3 cells, we identified more than 25 interchromosomal translocations of regions ≥ 200 kb on both micro- and macrochromosomes. We classified most of the observed translocations as unbalanced, leading to the formation of heteromorphic chromosomes. In many cases of microchromosome rearrangements, an entire microchromosome together with other macro- and microchromosomes participated in the emergence of a derivative chromosome, resembling "chromosomal fusions'' between acrocentric microchromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Several of the identified simple and complex chromosomal rearrangements, such as between GGA2 and GGA1qter; GGA5, GGA4p and GGA7p; GGA4q, GGA6 and GGA19; and duplication of the sex chromosome GGAW, were confirmed by FISH. CONCLUSIONS In the erythroid progenitor HD3 cell line, in contrast to mature and immature erythrocytes, the genome is organized into distinct topologically associating domains. The HD3 cell line has a severely rearranged karyotype with most of the chromosomes engaged in translocations and can be used in studies of genome structure-function relationships. Hi-C proved to be a reliable tool for simultaneous assessment of the spatial genome organization and chromosomal aberrations in karyotypes of birds with a large number of microchromosomes.
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Affiliation(s)
- A. Maslova
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
| | - V. Plotnikov
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
| | - M. Nuriddinov
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - M. Gridina
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - V. Fishman
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - A. Krasikova
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
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Boyd RJ, McClymont SA, Barrientos NB, Hook PW, Law WD, Rose RJ, Waite EL, Avramopoulos D, McCallion AS. Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525270. [PMID: 36747739 PMCID: PMC9900784 DOI: 10.1101/2023.01.23.525270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To overcome the ethical and technical limitations of in vivo human disease models, the broader scientific community frequently employs model organism-derived cell lines to investigate of disease mechanisms, pathways, and therapeutic strategies. Despite the widespread use of certain in vitro models, many still lack contemporary genomic analysis supporting their use as a proxy for the affected human cells and tissues. Consequently, it is imperative to determine how accurately and effectively any proposed biological surrogate may reflect the biological processes it is assumed to model. One such cellular surrogate of human disease is the established mouse neural precursor cell line, SN4741, which has been used to elucidate mechanisms of neurotoxicity in Parkinson disease for over 25 years. Here, we are using a combination of classic and contemporary genomic techniques - karyotyping, RT-qPCR, single cell RNA-seq, bulk RNA-seq, and ATAC-seq - to characterize the transcriptional landscape, chromatin landscape, and genomic architecture of this cell line, and evaluate its suitability as a proxy for midbrain dopaminergic neurons in the study of Parkinson disease. We find that SN4741 cells possess an unstable triploidy and consistently exhibits low expression of dopaminergic neuron markers across assays, even when the cell line is shifted to the non-permissive temperature that drives differentiation. The transcriptional signatures of SN4741 cells suggest that they are maintained in an undifferentiated state at the permissive temperature and differentiate into immature neurons at the non-permissive temperature; however, they may not be dopaminergic neuron precursors, as previously suggested. Additionally, the chromatin landscapes of SN4741 cells, in both the differentiated and undifferentiated states, are not concordant with the open chromatin profiles of ex vivo , mouse E15.5 forebrain- or midbrain-derived dopaminergic neurons. Overall, our data suggest that SN4741 cells may reflect early aspects of neuronal differentiation but are likely not a suitable a proxy for dopaminergic neurons as previously thought. The implications of this study extend broadly, illuminating the need for robust biological and genomic rationale underpinning the use of in vitro models of molecular processes.
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Affiliation(s)
- Rachel J. Boyd
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sarah A. McClymont
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nelson B. Barrientos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Paul W. Hook
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William D. Law
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rebecca J. Rose
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric L. Waite
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dimitrios Avramopoulos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew S. McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Three-dimensional chromatin architecture datasets for aging and Alzheimer's disease. Sci Data 2023; 10:51. [PMID: 36693875 PMCID: PMC9873630 DOI: 10.1038/s41597-023-01948-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/10/2023] [Indexed: 01/25/2023] Open
Abstract
Recently, increasing studies are indicating a close association between dysregulated enhancers and neurodegenerative diseases, such as Alzheimer's disease (AD). However, their contributions were poorly defined for lacking direct links to disease genes. To bridge this gap, we presented the Hi-C datasets of 4 AD patients, 4 dementia-free aged and 3 young subjects, including 30 billion reads. As applications, we utilized them to link the AD risk SNPs and dysregulated epigenetic marks to the target genes. Combining with epigenetic data, we observed more detailed interactions among regulatory regions and found that many known AD risk genes were under long-distance promoter-enhancer interactions. For future AD and aging studies, our datasets provide a reference landscape to better interpret findings of association and epigenetic studies for AD and aging process.
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