1
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Xu Y, Das P, McCord RP, Shen T. Node features of chromosome structure networks and their connections to genome annotation. Comput Struct Biotechnol J 2024; 23:2240-2250. [PMID: 38827231 PMCID: PMC11140560 DOI: 10.1016/j.csbj.2024.05.026] [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: 12/13/2023] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/04/2024] Open
Abstract
The 3D conformations of chromosomes can encode biological significance, and the implications of such structures have been increasingly appreciated recently. Certain chromosome structural features, such as A/B compartmentalization, are frequently extracted from Hi-C pairwise genome contact information (physical association between different regions of the genome) and compared with linear annotations of the genome, such as histone modifications and lamina association. We investigate how additional properties of chromosome structure can be deduced using an abstract graph representation of the contact heatmap, and describe specific network properties that can have a strong connection with some of these biological annotations. We constructed chromosome structure networks (CSNs) from bulk Hi-C data and calculated a set of site-resolved (node-based) network properties. These properties are useful for characterizing certain aspects of chromosomal structure. We examined the ability of network properties to differentiate several scenarios, such as haploid vs diploid cells, partially inverted nuclei vs conventional architecture, depletion of chromosome architectural proteins, and structural changes during cell development. We also examined the connection between network properties and a series of other linear annotations, such as histone modifications and chromatin states including poised promoter and enhancer labels. We found that semi-local network properties exhibit greater capability in characterizing genome annotations compared to diffusive or ultra-local node features. For example, the local square clustering coefficient can be a strong classifier of lamina-associated domains. We demonstrated that network properties can be useful for highlighting large-scale chromosome structure differences that emerge in different biological situations.
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Affiliation(s)
- Yingjie Xu
- Graduate School of Genome Science & Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Priyojit Das
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
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2
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Hibino K, Sakai Y, Tamura S, Takagi M, Minami K, Natsume T, Shimazoe MA, Kanemaki MT, Imamoto N, Maeshima K. Single-nucleosome imaging unveils that condensins and nucleosome-nucleosome interactions differentially constrain chromatin to organize mitotic chromosomes. Nat Commun 2024; 15:7152. [PMID: 39169041 DOI: 10.1038/s41467-024-51454-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
For accurate mitotic cell division, replicated chromatin must be assembled into chromosomes and faithfully segregated into daughter cells. While protein factors like condensin play key roles in this process, it is unclear how chromosome assembly proceeds as molecular events of nucleosomes in living cells and how condensins act on nucleosomes to organize chromosomes. To approach these questions, we investigate nucleosome behavior during mitosis of living human cells using single-nucleosome tracking, combined with rapid-protein depletion technology and computational modeling. Our results show that local nucleosome motion becomes increasingly constrained during mitotic chromosome assembly, which is functionally distinct from condensed apoptotic chromatin. Condensins act as molecular crosslinkers, locally constraining nucleosomes to organize chromosomes. Additionally, nucleosome-nucleosome interactions via histone tails constrain and compact whole chromosomes. Our findings elucidate the physical nature of the chromosome assembly process during mitosis.
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Affiliation(s)
- Kayo Hibino
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Yuji Sakai
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masatoshi Takagi
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Toyoaki Natsume
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masa A Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Masato T Kanemaki
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan.
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3
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Shi C, Liu L, Hyeon C. Hi-C-guided many-polymer model to decipher 3D genome organization. Biophys J 2024; 123:2574-2583. [PMID: 38932457 DOI: 10.1016/j.bpj.2024.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/27/2024] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
We propose a high-throughput chromosome conformation capture data-based many-polymer model that allows us to generate an ensemble of multi-scale genome structures. We demonstrate the efficacy of our model by validating the generated structures against experimental measurements and employ them to address key questions regarding genome organization. Our model first confirms a significant correlation between chromosome size and nuclear positioning. Specifically, smaller chromosomes are distributed at the core region, whereas larger chromosomes are at the periphery, interacting with the nuclear envelope. The spatial distribution of A- and B-type compartments, which is nontrivial to infer from the corresponding high-throughput chromosome conformation capture maps alone, can also be elucidated using our model, accounting for an issue such as the effect of chromatin-lamina interaction on the compartmentalization of conventional and inverted nuclei. In accordance with imaging data, the overall shape of the 3D genome structures generated from our model displays significant variation. As a case study, we apply our method to the yellow fever mosquito genome, finding that the predicted morphology displays, on average, a more globular shape than the previously suggested spindle-like organization and that our prediction better aligns with the fluorescence in situ hybridization data. Our model has great potential to be extended to investigate many outstanding issues concerning 3D genome organization.
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Affiliation(s)
- Chen Shi
- Key Laboratory of Optical Field Manipulation of Zhejiang Province, Department of Physics, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lei Liu
- Key Laboratory of Optical Field Manipulation of Zhejiang Province, Department of Physics, Zhejiang Sci-Tech University, Hangzhou, China.
| | - Changbong Hyeon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
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4
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Raynal F, Sengupta K, Plewczynski D, Aliaga B, Pancaldi V. Global chromatin reorganization and regulation of genes of specific evolutionary age in differentiation and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.30.564438. [PMID: 39149250 PMCID: PMC11326123 DOI: 10.1101/2023.10.30.564438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Oncogenesis is accompanied by chromatin organization alterations and reactivation of unicellular phenotypes at the metabolic and transcriptional level. The mechanisms connecting these two observations are unexplored, despite its relevance in cancer biology. Assigning evolutionary ages to genes in the context of 3D chromatin structure, we characterize the epigenomic landscape, expression regulation and spatial organization of genes according to their evolutionary ages. We describe topological changes across differentiation and find some of the patterns, involving Polycomb repression and RNA Pol II pausing, being reversed during oncogenesis. Going beyond the evidence of non-random organization of genes and chromatin features in the 3D epigenome, we suggest that these patterns lead to preferential interactions of old, intermediate and young genes, mediated by respectively RNA Polymerase II, Polycomb and the lamina. Our results are in line and expand recent findings implicating loss of Polycomb repression and activation of embryonal and early evolutionary programs in cancer.
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Affiliation(s)
- Flavien Raynal
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Kaustav Sengupta
- Laboratory of Functional and Structural Genomics, Center of New Technologies (CeNT), University of Warsaw, Mazowieckie, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dariusz Plewczynski
- Laboratory of Functional and Structural Genomics, Center of New Technologies (CeNT), University of Warsaw, Mazowieckie, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Benoît Aliaga
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Vera Pancaldi
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
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5
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Keikhosravi A, Almansour F, Bohrer CH, Fursova NA, Guin K, Sood V, Misteli T, Larson DR, Pegoraro G. High-throughput image processing software for the study of nuclear architecture and gene expression. Sci Rep 2024; 14:18426. [PMID: 39117696 PMCID: PMC11310328 DOI: 10.1038/s41598-024-66600-1] [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: 10/27/2023] [Accepted: 07/02/2024] [Indexed: 08/10/2024] Open
Abstract
High-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software programs for image analysis workflows typically do not allow full customization and adoption of new image processing algorithms in the analysis modules. While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis modules or algorithms. Here, we introduce the High-Throughput Image Processing Software (HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS incorporates advanced image processing and machine learning algorithms for automated cell and nuclei segmentation, spot signal detection, nucleus tracking, nucleus registration, spot tracking, and quantification of spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to integration of new analysis modules for existing analysis pipelines and to adding new analysis modules. To demonstrate the utility of HiTIPS, we present three examples of image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-friendly, flexible, and open-source HTI software platform for a variety of cell biology applications.
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Affiliation(s)
- Adib Keikhosravi
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Faisal Almansour
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical School, Washington, DC, 20057, USA
| | - Christopher H Bohrer
- System Biology of Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Nadezda A Fursova
- System Biology of Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Krishnendu Guin
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Varun Sood
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
- System Biology of Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Daniel R Larson
- System Biology of Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
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6
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Mohan AV, Escuer P, Cornet C, Lucek K. A three-dimensional genomics view for speciation research. Trends Genet 2024; 40:638-641. [PMID: 38880723 DOI: 10.1016/j.tig.2024.05.009] [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: 03/07/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024]
Abstract
Genomic information is folded in a three-dimensional (3D) structure, a rarely explored evolutionary driver of speciation. Technological advances now enable the study of 3D genome structures (3DGSs) across the Tree of Life. At the onset of 3D speciation genomics, we discuss the putative roles of 3DGSs in speciation.
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Affiliation(s)
- Ashwini V Mohan
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
| | - Paula Escuer
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Camille Cornet
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Kay Lucek
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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7
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Das M, Semple JI, Haemmerli A, Volodkina V, Scotton J, Gitchev T, Annan A, Campos J, Statzer C, Dakhovnik A, Ewald CY, Mozziconacci J, Meister P. Condensin I folds the Caenorhabditis elegans genome. Nat Genet 2024:10.1038/s41588-024-01832-5. [PMID: 39039278 DOI: 10.1038/s41588-024-01832-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/13/2024] [Indexed: 07/24/2024]
Abstract
The structural maintenance of chromosome (SMC) complexes-cohesin and condensins-are crucial for chromosome separation and compaction during cell division. During the interphase, mammalian cohesins additionally fold the genome into loops and domains. Here we show that, in Caenorhabditis elegans, a species with holocentric chromosomes, condensin I is the primary, long-range loop extruder. The loss of condensin I and its X-specific variant, condensin IDC, leads to genome-wide decompaction, chromosome mixing and disappearance of X-specific topologically associating domains, while reinforcing fine-scale epigenomic compartments. In addition, condensin I/IDC inactivation led to the upregulation of X-linked genes and unveiled nuclear bodies grouping together binding sites for the X-targeting loading complex of condensin IDC. C. elegans condensin I/IDC thus uniquely organizes holocentric interphase chromosomes, akin to cohesin in mammals, as well as regulates X-chromosome gene expression.
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Affiliation(s)
- Moushumi Das
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Jennifer I Semple
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Anja Haemmerli
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Valeriia Volodkina
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Janik Scotton
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Todor Gitchev
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Ahrmad Annan
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Julie Campos
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Cyril Statzer
- Eidgenössische Technische Hochschule Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, Schwerzenbach, Switzerland
| | - Alexander Dakhovnik
- Eidgenössische Technische Hochschule Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, Schwerzenbach, Switzerland
| | - Collin Y Ewald
- Eidgenössische Technische Hochschule Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, Schwerzenbach, Switzerland
| | - Julien Mozziconacci
- Laboratoire Structure et Instabilité des Génomes UMR 7196, Muséum National d'Histoire Naturelle, Paris, France
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland.
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8
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Sandoval-Velasco M, Dudchenko O, Rodríguez JA, Pérez Estrada C, Dehasque M, Fontsere C, Mak SST, Khan R, Contessoto VG, Oliveira Junior AB, Kalluchi A, Zubillaga Herrera BJ, Jeong J, Roy RP, Christopher I, Weisz D, Omer AD, Batra SS, Shamim MS, Durand NC, O'Connell B, Roca AL, Plikus MV, Kusliy MA, Romanenko SA, Lemskaya NA, Serdyukova NA, Modina SA, Perelman PL, Kizilova EA, Baiborodin SI, Rubtsov NB, Machol G, Rath K, Mahajan R, Kaur P, Gnirke A, Garcia-Treviño I, Coke R, Flanagan JP, Pletch K, Ruiz-Herrera A, Plotnikov V, Pavlov IS, Pavlova NI, Protopopov AV, Di Pierro M, Graphodatsky AS, Lander ES, Rowley MJ, Wolynes PG, Onuchic JN, Dalén L, Marti-Renom MA, Gilbert MTP, Aiden EL. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell 2024; 187:3541-3562.e51. [PMID: 38996487 DOI: 10.1016/j.cell.2024.06.002] [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: 06/30/2023] [Revised: 03/07/2024] [Accepted: 06/03/2024] [Indexed: 07/14/2024]
Abstract
Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.
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Affiliation(s)
| | - Olga Dudchenko
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
| | - Juan Antonio Rodríguez
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain
| | - Cynthia Pérez Estrada
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Marianne Dehasque
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Ruqayya Khan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Bernardo J Zubillaga Herrera
- Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA
| | - Jiyun Jeong
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Renata P Roy
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Departments of Biology and Physics, Texas Southern University, Houston, TX 77004, USA
| | - Ishawnia Christopher
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sanjit S Batra
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neva C Durand
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alfred L Roca
- Department of Animal Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mariya A Kusliy
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | | | - Natalya A Lemskaya
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | | | - Svetlana A Modina
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | - Elena A Kizilova
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | | | - Nikolai B Rubtsov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Gur Machol
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Krisha Rath
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009, Australia
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Rob Coke
- San Antonio Zoo, San Antonio, TX 78212, USA
| | | | | | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia and Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | | | - Naryya I Pavlova
- Institute of Biological Problems of Cryolitezone SB RAS, Yakutsk 677000, Russia
| | - Albert V Protopopov
- Academy of Sciences of Sakha Republic, Yakutsk 677000, Russia; North-Eastern Federal University, Yakutsk 677027, Russia
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA
| | | | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA
| | - Love Dalén
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marc A Marti-Renom
- Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain; Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain.
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway.
| | - Erez Lieberman Aiden
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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9
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Gil J, Rosin LF, Navarrete E, Chowdhury N, Abraham S, Cornilleau G, Lei EP, Mozziconacci J, Mirny LA, Muller H, Drinnenberg IA. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557757. [PMID: 37745315 PMCID: PMC10515926 DOI: 10.1101/2023.09.14.557757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and insulated domains, including topologically associated domains (TADs). Yet, most of these elements of chromosome organization are derived from analyses of a limited set of model organisms, while large eukaryotic groups, including insects, remain mostly unexplored. Here we combine Hi-C, biophysical modeling, and microscopy to characterize the 3D genome architecture of the silkworm, Bombyx mori. In contrast to other eukaryotes, B. mori chromosomes form highly separated territories. Similar to other eukaryotes, B. mori chromosomes segregate into active A and inactive B compartments, yet unlike in vertebrate systems, contacts between euchromatic A regions appear to be a strong driver of compartmentalization. Remarkably, we also identify a third compartment, called secluded S, with a unique contact pattern. Each S region shows prominent short-range self-contacts and is remarkably devoid of contacts with the rest of the chromosome, including other S regions. Compartment S hosts a unique combination of genetic and epigenetic features, localizes towards the periphery of CTs, and shows developmental plasticity. Biophysical modeling reveals that the formation of such secluded domains requires highly localized loop extrusion within them, along with a low level of extrusion in A and B. Our Hi-C data supports predicted genome-wide and localized extrusion. Such a broad, non-uniform distribution of extruders has not been seen in other organisms. Overall, our analyses support loop extrusion in insects and highlight the evolutionary plasticity of 3D genome organization, driven by a new combination of known processes.
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10
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Sugiura K, Yoshida Y, Hayashi K, Arakawa K, Kunieda T, Matsumoto M. Sexual dimorphism in the tardigrade Paramacrobiotus metropolitanus transcriptome. ZOOLOGICAL LETTERS 2024; 10:11. [PMID: 38902818 PMCID: PMC11191345 DOI: 10.1186/s40851-024-00233-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND In gonochoristic animals, the sex determination pathway induces different morphological and behavioral features that can be observed between sexes, a condition known as sexual dimorphism. While many components of this sex differentiation cascade show high levels of diversity, factors such as the Doublesex-Mab-3-Related Transcription factor (DMRT) are widely conserved across animal taxa. Species of the phylum Tardigrada exhibit remarkable diversity in morphology and behavior between sexes, suggesting a pathway regulating this dimorphism. Despite the wealth of genomic and zoological knowledge accumulated in recent studies, the sexual differences in tardigrades genomes have not been identified. In the present study, we focused on the gonochoristic species Paramacrobiotus metropolitanus and employed omics analyses to unravel the molecular basis of sexual dimorphism. RESULTS Transcriptome analysis between sex-identified specimens revealed numerous differentially expressed genes, of which approximately 2,000 male-biased genes were focused on 29 non-male-specific genomic loci. From these regions, we identified two Macrobiotidae family specific DMRT paralogs, which were significantly upregulated in males and lacked sex specific splicing variants. Furthermore, phylogenetic analysis indicated all tardigrade genomes lack the doublesex ortholog, suggesting doublesex emerged after the divergence of Tardigrada. In contrast to sex-specific expression, no evidence of genomic differences between the sexes was found. We also identified several anhydrobiosis genes that exhibit sex-biased expression, suggesting a possible mechanism for protection of sex-specific tissues against extreme stress. CONCLUSIONS This study provides a comprehensive analysis for analyzing the genetic differences between sexes in tardigrades. The existence of male-biased, but not male-specific, genomic loci and identification of the family specific male-biased DMRT subfamily provides the foundation for understanding the sex determination cascade. In addition, sex-biased expression of several tardigrade-specific genes which are involved their stress tolerance suggests a potential role in protecting sex-specific tissue and gametes.
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Affiliation(s)
- Kenta Sugiura
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yuki Yoshida
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Kohei Hayashi
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, 403-1 Nihonkoku, Daihoji, Tsuruoka, Yamagata, 997-0017, Japan
- Exploratory Research Center On Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Takekazu Kunieda
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Midori Matsumoto
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan.
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11
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Long Y, Wendel JF, Zhang X, Wang M. Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants. TRENDS IN PLANT SCIENCE 2024; 29:638-649. [PMID: 38061928 DOI: 10.1016/j.tplants.2023.11.009] [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: 08/24/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 06/09/2024]
Abstract
Development of complex traits necessitates the functioning and coordination of intricate regulatory networks involving multiple genes. Understanding 3D chromatin structure can facilitate insight into the regulation of gene expression by regulatory elements. This potential, of visualizing the role of chromatin organization in the evolution and function of regulatory elements, remains largely unexplored. Here, we describe new perspectives that arise from the dual considerations of sequence variation of regulatory elements and chromatin structure, with a special focus on whole-genome doubling or polyploidy. We underscore the significance of hierarchical chromatin organization in gene regulation during evolution. In addition, we describe strategies for exploring chromatin organization in future investigations of regulatory evolution in plants, enabling insights into the evolutionary influence of regulatory elements on gene expression and, hence, phenotypes.
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Affiliation(s)
- Yuexuan Long
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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12
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Câmara AS, Kubalová I, Schubert V. Helical chromonema coiling is conserved in eukaryotes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1284-1300. [PMID: 37840457 DOI: 10.1111/tpj.16484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023]
Abstract
Efficient chromatin condensation is required to transport chromosomes during mitosis and meiosis, forming daughter cells. While it is well accepted that these processes follow fundamental rules, there has been a controversial debate for more than 140 years on whether the higher-order chromatin organization in chromosomes is evolutionarily conserved. Here, we summarize historical and recent investigations based on classical and modern methods. In particular, classical light microscopy observations based on living, fixed, and treated chromosomes covering a wide range of plant and animal species, and even in single-cell eukaryotes suggest that the chromatids of large chromosomes are formed by a coiled chromatin thread, named the chromonema. More recently, these findings were confirmed by electron and super-resolution microscopy, oligo-FISH, molecular interaction data, and polymer simulation. Altogether, we describe common and divergent features of coiled chromonemata in different species. We hypothesize that chromonema coiling in large chromosomes is a fundamental feature established early during the evolution of eukaryotes to handle increasing genome sizes.
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Affiliation(s)
- Amanda Souza Câmara
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
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13
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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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14
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Shao W, Wang J, Zhang Y, Zhang C, Chen J, Chen Y, Fei Z, Ma Z, Sun X, Jiao C. The jet-like chromatin structure defines active secondary metabolism in fungi. Nucleic Acids Res 2024; 52:4906-4921. [PMID: 38407438 PMCID: PMC11109943 DOI: 10.1093/nar/gkae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
Eukaryotic genomes are spatially organized within the nucleus in a nonrandom manner. However, fungal genome arrangement and its function in development and adaptation remain largely unexplored. Here, we show that the high-order chromosome structure of Fusarium graminearum is sculpted by both H3K27me3 modification and ancient genome rearrangements. Active secondary metabolic gene clusters form a structure resembling chromatin jets. We demonstrate that these jet-like domains, which can propagate symmetrically for 54 kb, are prevalent in the genome and correlate with active gene transcription and histone acetylation. Deletion of GCN5, which encodes a core and functionally conserved histone acetyltransferase, blocks the formation of the domains. Insertion of an exogenous gene within the jet-like domain significantly augments its transcription. These findings uncover an interesting link between alterations in chromatin structure and the activation of fungal secondary metabolism, which could be a general mechanism for fungi to rapidly respond to environmental cues, and highlight the utility of leveraging three-dimensional genome organization in improving gene transcription in eukaryotes.
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Affiliation(s)
- Wenyong Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jingrui Wang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yueqi Zhang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chaofan Zhang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Jie Chen
- National Joint Engineering Laboratory of Biopesticide Preparation, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Chen Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
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15
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Moreno JA, Dudchenko O, Feigin CY, Mereby SA, Chen Z, Ramos R, Almet AA, Sen H, Brack BJ, Johnson MR, Li S, Wang W, Gaska JM, Ploss A, Weisz D, Omer AD, Yao W, Colaric Z, Kaur P, Leger JS, Nie Q, Mena A, Flanagan JP, Keller G, Sanger T, Ostrow B, Plikus MV, Kvon EZ, Aiden EL, Mallarino R. Emx2 underlies the development and evolution of marsupial gliding membranes. Nature 2024; 629:127-135. [PMID: 38658750 PMCID: PMC11062917 DOI: 10.1038/s41586-024-07305-3] [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: 03/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium-an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.
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Affiliation(s)
- Jorge A Moreno
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Charles Y Feigin
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Environment and Genetics, La Trobe University, Bundoora, Victoria, Australia
| | - Sarah A Mereby
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Zhuoxin Chen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Raul Ramos
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Harsha Sen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Benjamin J Brack
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew R Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sha Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Lewis Sigler Center for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jenna M Gaska
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weijie Yao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Parwinder Kaur
- The University of Western Australia, Crawley, Western Australia, Australia
| | - Judy St Leger
- Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | | | | | - Greta Keller
- Department of Biology, Loyola University, Chicago, IL, USA
| | - Thomas Sanger
- Department of Biology, Loyola University, Chicago, IL, USA
| | - Bruce Ostrow
- Department of Biology, Grand Valley State University, Allendale, MI, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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16
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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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17
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Plessy C, Mansfield MJ, Bliznina A, Masunaga A, West C, Tan Y, Liu AW, Grašič J, Del Río Pisula MS, Sánchez-Serna G, Fabrega-Torrus M, Ferrández-Roldán A, Roncalli V, Navratilova P, Thompson EM, Onuma T, Nishida H, Cañestro C, Luscombe NM. Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. Genome Res 2024; 34:426-440. [PMID: 38621828 PMCID: PMC11067885 DOI: 10.1101/gr.278295.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
Abstract
Genome structural variations within species are rare. How selective constraints preserve gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several genomes of the appendicularian tunicate Oikopleura dioica around the globe reveals extreme genome scrambling caused by thousands of chromosomal rearrangements, although showing no obvious morphological differences between these animals. The breakpoint accumulation rate is an order of magnitude higher than in ascidian tunicates, nematodes, Drosophila, or mammals. Chromosome arms and sex-specific regions appear to be the primary unit of macrosynteny conservation. At the microsyntenic level, scrambling did not preserve operon structures, suggesting an absence of selective pressure to maintain them. The uncoupling of the genome scrambling with morphological conservation in O. dioica suggests the presence of previously unnoticed cryptic species and provides a new biological system that challenges our previous vision of speciation in which similar animals always share similar genome structures.
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Affiliation(s)
- Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan;
| | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Aleksandra Bliznina
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Aki Masunaga
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Charlotte West
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Yongkai Tan
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Andrew W Liu
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Jan Grašič
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - María Sara Del Río Pisula
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Gaspar Sánchez-Serna
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Marc Fabrega-Torrus
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Alfonso Ferrández-Roldán
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Vittoria Roncalli
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Pavla Navratilova
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, 779 00 Olomouc, Czech Republic
- Sars International Centre, University of Bergen, Bergen N-5008, Norway
| | - Eric M Thompson
- Sars International Centre, University of Bergen, Bergen N-5008, Norway
- Department of Biological Sciences, University of Bergen, Bergen N-5020, Norway
| | - Takeshi Onuma
- Faculty of Science, Kagoshima University, Kagoshima 890-0065, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
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18
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Torralba Sáez M, Hofreiter M, Straube N. Shark genome size evolution and its relationship with cellular, life-history, ecological, and diversity traits. Sci Rep 2024; 14:8909. [PMID: 38632352 PMCID: PMC11024215 DOI: 10.1038/s41598-024-59202-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Among vertebrates, sharks exhibit both large and heterogeneous genome sizes ranging from 2.86 to 17.05 pg. Aiming for a better understanding of the patterns and causalities of shark genome size evolution, we applied phylogenetic comparative methods to published genome-size estimates for 71 species representing the main phylogenetic lineages, life-histories and ecological traits. The sixfold range of genome size variation was strongly traceable throughout the phylogeny, with a major expansion preceding shark diversification during the late Paleozoic and an ancestral state (6.33 pg) close to the present-day average (6.72 pg). Subsequent deviations from this average occurred at higher rates in squalomorph than in galeomorph sharks and were unconnected to evolutionary changes in the karyotype architecture, which were dominated by descending disploidy events. Genome size was positively correlated with cell and nucleus sizes and negatively with metabolic rate. The metabolic constraints on increasing genome size also manifested at higher phenotypic scales, with large genomes associated with slow lifestyles and purely marine waters. Moreover, large genome sizes were also linked to non-placental reproductive modes, which may entail metabolically less demanding embryological developments. Contrary to ray-finned fishes, large genome size was associated neither with the taxonomic diversity of affected clades nor with low genetic diversity.
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Affiliation(s)
- Mario Torralba Sáez
- Ichthyology Section, Bavarian State Collection of Zoology (SNSB-ZSM), 81247, Munich, Germany
- Systematic Zoology, Department Biology II, Faculty of Biology, Ludwig Maximilian University of Munich (LMU), 82152, Munich, Germany
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Nicolas Straube
- Department of Natural History, University Museum Bergen, University of Bergen (UiB), 5007, Bergen, Norway.
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19
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Golov AK, Gavrilov AA. Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:601-625. [PMID: 38831499 DOI: 10.1134/s0006297924040023] [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: 10/21/2023] [Revised: 12/29/2023] [Accepted: 02/15/2024] [Indexed: 06/05/2024]
Abstract
The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion. This review briefly summarizes the current understanding of the place and role of cohesin-dependent extrusion in cell physiology and presents a number of models describing the potential molecular mechanism of extrusion in a most compelling way. We conclude the review with a discussion of how the capacity of cohesin to extrude DNA loops may be mechanistically linked to its involvement in sister chromatid cohesion.
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Affiliation(s)
- Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Technion - Israel Institute of Technology, Haifa, 3525433, Israel
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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20
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da Roza PA, Muller H, Sullivan GJ, Walker RSK, Goold HD, Willows RD, Palenik B, Paulsen IT. Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C 4 photosynthesis. Microb Genom 2024; 10. [PMID: 38625719 DOI: 10.1099/mgen.0.001223] [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: 04/17/2024] Open
Abstract
Genome sequencing and assembly of the photosynthetic picoeukaryotic Picochlorum sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins, as compared to similarly sized marine picoprasinophytes Mamiellales, and broad halotolerance compared to others in Trebouxiophyceae, suggests evolutionary adaptation to variable salinity environments. Such adaptation may have driven size and genome minimization and have been enabled by the retention of a high number of membrane transporters. Identification of required pathway genes for both CAM and C4 photosynthetic carbon fixation, known to exist in the marine mamiellale pico-prasinophytes and seaweed Ulva, but few other chlorophyte species, further highlights the unique adaptations of this robust alga. This high-quality assembly provides a significant advance in the resources available for genomic investigations of this and other photosynthetic picoeukaryotes.
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Affiliation(s)
- Patrick A da Roza
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Héloïse Muller
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - Geraldine J Sullivan
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Roy S K Walker
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Hugh D Goold
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia
| | - Robert D Willows
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
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21
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Lin Y, Li J, Gu Y, Jin L, Bai J, Zhang J, Wang Y, Liu P, Long K, He M, Li D, Liu C, Han Z, Zhang Y, Li X, Zeng B, Lu L, Kong F, Sun Y, Fan Y, Wang X, Wang T, Jiang A, Ma J, Shen L, Zhu L, Jiang Y, Tang G, Fan X, Liu Q, Li H, Wang J, Chen L, Ge L, Li X, Tang Q, Li M. Haplotype-resolved 3D chromatin architecture of the hybrid pig. Genome Res 2024; 34:310-325. [PMID: 38479837 PMCID: PMC10984390 DOI: 10.1101/gr.278101.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter-enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.
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Affiliation(s)
- Yu Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
| | - Yiren Gu
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingyi Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yujie Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Pengliang Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mengnan He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Can Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ziyin Han
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaokai Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Zeng
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lu Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Fanli Kong
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ying Sun
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Geriatric Health, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yongliang Fan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - An'an Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jideng Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanzhi Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoqing Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaolan Fan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qingyou Liu
- Animal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Hua Li
- Animal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jinyong Wang
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Li Chen
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Liangpeng Ge
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Xuewei Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianzi Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
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22
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Fisher AG. Cell and developmental biology: grand challenges. Front Cell Dev Biol 2024; 12:1377073. [PMID: 38559812 PMCID: PMC10978741 DOI: 10.3389/fcell.2024.1377073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Affiliation(s)
- Amanda G. Fisher
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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23
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Patta I, Zand M, Lee L, Mishra S, Bortnick A, Lu H, Prusty A, McArdle S, Mikulski Z, Wang HY, Cheng CS, Fisch KM, Hu M, Murre C. Nuclear morphology is shaped by loop-extrusion programs. Nature 2024; 627:196-203. [PMID: 38355805 PMCID: PMC11052650 DOI: 10.1038/s41586-024-07086-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/17/2024] [Indexed: 02/16/2024]
Abstract
It is well established that neutrophils adopt malleable polymorphonuclear shapes to migrate through narrow interstitial tissue spaces1-3. However, how polymorphonuclear structures are assembled remains unknown4. Here we show that in neutrophil progenitors, halting loop extrusion-a motor-powered process that generates DNA loops by pulling in chromatin5-leads to the assembly of polymorphonuclear genomes. Specifically, we found that in mononuclear neutrophil progenitors, acute depletion of the loop-extrusion loading factor nipped-B-like protein (NIPBL) induced the assembly of horseshoe, banded, ringed and hypersegmented nuclear structures and led to a reduction in nuclear volume, mirroring what is observed during the differentiation of neutrophils. Depletion of NIPBL also induced cell-cycle arrest, activated a neutrophil-specific gene program and conditioned a loss of interactions across topologically associating domains to generate a chromatin architecture that resembled that of differentiated neutrophils. Removing NIPBL resulted in enrichment for mega-loops and interchromosomal hubs that contain genes associated with neutrophil-specific enhancer repertoires and an inflammatory gene program. On the basis of these observations, we propose that in neutrophil progenitors, loop-extrusion programs produce lineage-specific chromatin architectures that permit the packing of chromosomes into geometrically confined lobular structures. Our data also provide a blueprint for the assembly of polymorphonuclear structures, and point to the possibility of engineering de novo nuclear shapes to facilitate the migration of effector cells in densely populated tumorigenic environments.
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Affiliation(s)
- Indumathi Patta
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Maryam Zand
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Lindsay Lee
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Shreya Mishra
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Alexandra Bortnick
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Hanbin Lu
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Arpita Prusty
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Sara McArdle
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Huan-You Wang
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Christine S Cheng
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
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24
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Ito N, Sakamoto T, Oko Y, Sato H, Hanamata S, Sakamoto Y, Matsunaga S. Nuclear pore complex proteins are involved in centromere distribution. iScience 2024; 27:108855. [PMID: 38318384 PMCID: PMC10839643 DOI: 10.1016/j.isci.2024.108855] [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: 05/06/2023] [Revised: 11/28/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
The subnuclear distribution of centromeres is cooperatively regulated by condensin II and the linker of nucleoskeleton and cytoskeleton (LINC) complex. However, other nuclear membrane structures and nuclear proteins are probably involved in centromere dynamics and distribution. Here, we focused on the nuclear pore complex (NPC), which is known to regulate gene expression, transcription memory, and chromatin structure in addition to transport between the cytoplasm and nucleoplasm. We report here that some nucleoporins (Nups), including Nup85, Nup133, CG1, Nup93b, and NUA, are involved in centromere scattering in Arabidopsis thaliana. In addition, the centromere dynamics after metaphase in nup mutants were found to be similar to that of the condensin II mutant. Furthermore, both biochemical and genetic approaches showed that the Nups interact with the LINC complex. These results suggest that Nups regulate centromere scattering cooperatively with condensin II and the LINC complex.
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Affiliation(s)
- Nanami Ito
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Takuya Sakamoto
- Department of Science, Faculty of Science, Kanagawa University, Yokohama, Kanagawa 221-8686, Japan
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yuka Oko
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Hikaru Sato
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Shigeru Hanamata
- Department of Science, Faculty of Science, Kanagawa University, Yokohama, Kanagawa 221-8686, Japan
| | - Yuki Sakamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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25
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Iida S, Ide S, Tamura S, Tani T, Goto T, Shribak M, Maeshima K. Orientation-Independent-DIC imaging reveals that a transient rise in depletion force contributes to mitotic chromosome condensation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.11.566679. [PMID: 37986866 PMCID: PMC10659371 DOI: 10.1101/2023.11.11.566679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed into mitotic chromosomes. Although protein factors like condensins and topoisomerase IIα are involved in the assembly of mitotic chromosomes, the physical bases of the condensation process remain unclear. Depletion force/macromolecular crowding, an effective attractive force that arises between large structures in crowded environments around chromosomes, may contribute to the condensation process. To approach this issue, we investigated the "chromosome milieu" during mitosis of living human cells using orientation-independent-differential interference contrast (OI-DIC) module combined with a confocal laser scanning microscope, which is capable of precisely mapping optical path differences and estimating molecular densities. We found that the molecular density surrounding chromosomes increased with the progression from prometaphase to anaphase, concurring with chromosome condensation. However, the molecular density went down in telophase, when chromosome decondensation began. Changes in the molecular density around chromosomes by hypotonic or hypertonic treatment consistently altered the condensation levels of chromosomes. In vitro, native chromatin was converted into liquid droplets of chromatin in the presence of cations and a macromolecular crowder. Additional crowder made the chromatin droplets stiffer and more solid-like, with further condensation. These results suggest that a transient rise in depletion force, likely triggered by the relocation of macromolecules (proteins, RNAs and others) via nuclear envelope breakdown and also by a subsequent decrease in cell-volumes, contributes to mitotic chromosome condensation, shedding light on a new aspect of the condensation mechanism in living human cells.
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Affiliation(s)
- Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Tomomi Tani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka 563-8577, Japan
| | - Tatsuhiko Goto
- Research Center for Global Agromedicine and Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Michael Shribak
- Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543, USA
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
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26
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Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat Commun 2024; 15:579. [PMID: 38233380 PMCID: PMC10794172 DOI: 10.1038/s41467-023-43012-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/27/2023] [Indexed: 01/19/2024] Open
Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Kelly E Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA
| | - Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Kodiak C Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Laurent M Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael J Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Robert D Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John H Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA.
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
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27
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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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28
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Romanova DY, Moroz LL. Brief History of Placozoa. Methods Mol Biol 2024; 2757:103-122. [PMID: 38668963 DOI: 10.1007/978-1-0716-3642-8_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: 05/04/2024]
Abstract
Placozoans are morphologically the simplest free-living animals. They represent a unique window of opportunities to understand both the origin of the animal organization and the rules of life for the system and synthetic biology of the future. However, despite more than 100 years of their investigations, we know little about their organization, natural habitats, and life strategies. Here, we introduce this unique animal phylum and highlight some directions vital to broadening the frontiers of the biomedical sciences. In particular, understanding the genomic bases of placozoan biodiversity, cell identity, connectivity, reproduction, and cellular bases of behavior are critical hot spots for future studies.
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Affiliation(s)
- Daria Y Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russian Federation.
| | - Leonid L Moroz
- Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
- Whitney Laboratory for Marine Biosciences University of Florida, St. Augustine, FL, USA.
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29
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Moroz LL. Brief History of Ctenophora. Methods Mol Biol 2024; 2757:1-26. [PMID: 38668961 DOI: 10.1007/978-1-0716-3642-8_1] [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: 05/04/2024]
Abstract
Ctenophores are the descendants of the earliest surviving lineage of ancestral metazoans, predating the branch leading to sponges (Ctenophore-first phylogeny). Emerging genomic, ultrastructural, cellular, and systemic data indicate that virtually every aspect of ctenophore biology as well as ctenophore development are remarkably different from what is described in representatives of other 32 animal phyla. The outcome of this reconstruction is that most system-level components associated with the ctenophore organization result from convergent evolution. In other words, the ctenophore lineage independently evolved as high animal complexities with the astonishing diversity of cell types and structures as bilaterians and cnidarians. Specifically, neurons, synapses, muscles, mesoderm, through gut, sensory, and integrative systems evolved independently in Ctenophora. Rapid parallel evolution of complex traits is associated with a broad spectrum of unique ctenophore-specific molecular innovations, including alternative toolkits for making an animal. However, the systematic studies of ctenophores are in their infancy, and deciphering their remarkable morphological and functional diversity is one of the hot topics in biological research, with many anticipated surprises.
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Affiliation(s)
- Leonid L Moroz
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
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30
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Forte G, Boteva L, Conforto F, Gilbert N, Cook PR, Marenduzzo D. Bridging condensins mediate compaction of mitotic chromosomes. J Cell Biol 2024; 223:e202209113. [PMID: 37976091 PMCID: PMC10655892 DOI: 10.1083/jcb.202209113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 07/08/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Eukaryotic chromosomes compact during mitosis into elongated cylinders-and not the spherical globules expected of self-attracting long flexible polymers. This process is mainly driven by condensin-like proteins. Here, we present Brownian-dynamic simulations involving two types of such proteins with different activities. One, which we refer to as looping condensins, anchors long-lived chromatin loops to create bottlebrush structures. The second, referred to as bridging condensins, forms multivalent bridges between distant parts of these loops. We show that binding of bridging condensins leads to the formation of shorter and stiffer mitotic-like cylinders without requiring any additional energy input. These cylinders have several features matching experimental observations. For instance, the axial condensin backbone breaks up into clusters as found by microscopy, and cylinder elasticity qualitatively matches that seen in chromosome pulling experiments. Additionally, simulating global condensin depletion or local faulty condensin loading gives phenotypes seen experimentally and points to a mechanistic basis for the structure of common fragile sites in mitotic chromosomes.
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Affiliation(s)
- Giada Forte
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Lora Boteva
- MRC Human Genetics Unit, Western General Hospital, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Filippo Conforto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Nick Gilbert
- MRC Human Genetics Unit, Western General Hospital, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Peter R. Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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31
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Hsiao J, Deng LC, Moroz LL, Chalasani SH, Edsinger E. Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution. Methods Mol Biol 2024; 2757:461-490. [PMID: 38668979 PMCID: PMC11112408 DOI: 10.1007/978-1-0716-3642-8_19] [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] [Indexed: 05/16/2024]
Abstract
Understanding gene evolution across genomes and organisms, including ctenophores, can provide unexpected biological insights. It enables powerful integrative approaches that leverage sequence diversity to advance biomedicine. Sequencing and bioinformatic tools can be inexpensive and user-friendly, but numerous options and coding can intimidate new users. Distinct challenges exist in working with data from diverse species but may go unrecognized by researchers accustomed to gold-standard genomes. Here, we provide a high-level workflow and detailed pipeline to enable animal collection, single-molecule sequencing, and phylogenomic analysis of gene and species evolution. As a demonstration, we focus on (1) PacBio RNA-seq of the genome-sequenced ctenophore Mnemiopsis leidyi, (2) diversity and evolution of the mechanosensitive ion channel Piezo in genetic models and basal-branching animals, and (3) associated challenges and solutions to working with diverse species and genomes, including gene model updating and repair using single-molecule RNA-seq. We provide a Python Jupyter Notebook version of our pipeline (GitHub Repository: Ctenophore-Ocean-To-Tree-2023 https://github.com/000generic/Ctenophore-Ocean-To-Tree-2023 ) that can be run for free in the Google Colab cloud to replicate our findings or modified for specific or greater use. Our protocol enables users to design new sequencing projects in ctenophores, marine invertebrates, or other novel organisms. It provides a simple, comprehensive platform that can ease new user entry into running their evolutionary sequence analyses.
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Affiliation(s)
- Jan Hsiao
- Molecular Neurobiology Laboratory, Salk Institute for Biological Study, La Jolla, CA 92037
| | - Lola Chenxi Deng
- Molecular Neurobiology Laboratory, Salk Institute for Biological Study, La Jolla, CA 92037
| | - Leonid L. Moroz
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, 32080
- Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL32611
| | - Sreekanth H. Chalasani
- Molecular Neurobiology Laboratory, Salk Institute for Biological Study, La Jolla, CA 92037
| | - Eric Edsinger
- Molecular Neurobiology Laboratory, Salk Institute for Biological Study, La Jolla, CA 92037
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32
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Tourdot E, Grob S. Three-dimensional chromatin architecture in plants - General features and novelties. Eur J Cell Biol 2023; 102:151344. [PMID: 37562220 DOI: 10.1016/j.ejcb.2023.151344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades. Work in the animal field has led to significant advances in our general understanding on eukaryotic genome organization. This did not only bring along insights into how the 3D genome interacts with the epigenetic landscape and the transcriptional machinery but also how 3D genome architecture is relevant for fundamental developmental processes, such as cell differentiation. In parallel, the 3D organization of plant genomes have been extensively studied, which resulted in both congruent and novel findings, contributing to a more complete view on how eukaryotic genomes are organized in multiple dimensions. Plant genomes are remarkably diverse in size, composition, and ploidy. Furthermore, as intrinsically sessile organisms without the possibility to relocate to more favorable environments, plants have evolved an elaborate epigenetic repertoire to rapidly respond to environmental challenges. The diversity in genome organization and the complex epigenetic programs make plants ideal study subjects to acquire a better understanding on universal features and inherent constraints of genome organization. Furthermore, considering a wide range of species allows us to study the evolutionary crosstalk between the various levels of genome architecture. In this article, we aim at summarizing important findings on 3D genome architecture obtained in various plant species. These findings cover many aspects of 3D genome organization on a wide range of levels, from gene loops to topologically associated domains and to global 3D chromosome configurations. We present an overview on plant 3D genome organizational features that resemble those in animals and highlight facets that have only been observed in plants to date.
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Affiliation(s)
- Edouard Tourdot
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
| | - Stefan Grob
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
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33
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Poinsignon T, Gallopin M, Grognet P, Malagnac F, Lelandais G, Poulain P. 3D models of fungal chromosomes to enhance visual integration of omics data. NAR Genom Bioinform 2023; 5:lqad104. [PMID: 38058589 PMCID: PMC10696920 DOI: 10.1093/nargab/lqad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
The functions of eukaryotic chromosomes and their spatial architecture in the nucleus are reciprocally dependent. Hi-C experiments are routinely used to study chromosome 3D organization by probing chromatin interactions. Standard representation of the data has relied on contact maps that show the frequency of interactions between parts of the genome. In parallel, it has become easier to build 3D models of the entire genome based on the same Hi-C data, and thus benefit from the methodology and visualization tools developed for structural biology. 3D modeling of entire genomes leverages the understanding of their spatial organization. However, this opportunity for original and insightful modeling is underexploited. In this paper, we show how seeing the spatial organization of chromosomes can bring new perspectives to omics data integration. We assembled state-of-the-art tools into a workflow that goes from Hi-C raw data to fully annotated 3D models and we re-analysed public omics datasets available for three fungal species. Besides the well-described properties of the spatial organization of their chromosomes (Rabl conformation, hypercoiling and chromosome territories), our results highlighted (i) in Saccharomyces cerevisiae, the backbones of the cohesin anchor regions, which were aligned all along the chromosomes, (ii) in Schizosaccharomyces pombe, the oscillations of the coiling of chromosome arms throughout the cell cycle and (iii) in Neurospora crassa, the massive relocalization of histone marks in mutants of heterochromatin regulators. 3D modeling of the chromosomes brings new opportunities for visual integration of omics data. This holistic perspective supports intuition and lays the foundation for building new concepts.
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Affiliation(s)
- Thibault Poinsignon
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Mélina Gallopin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Pierre Grognet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Gaëlle Lelandais
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Pierre Poulain
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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34
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Scadden AW, Graybill AS, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD. Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa. Proc Natl Acad Sci U S A 2023; 120:e2311249120. [PMID: 37963248 PMCID: PMC10666030 DOI: 10.1073/pnas.2311249120] [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: 07/20/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023] Open
Abstract
Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungus Neurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain-like structures formed by heterochromatic region aggregation. However, insufficient data exist on how histone posttranslational modifications (PTMs), including acetylation, affect genome organization. In Neurospora, the HCHC complex [composed of the proteins HDA-1, CDP-2 (Chromodomain Protein-2), Heterochromatin Protein-1, and CHAP (CDP-2 and HDA-1 Associated Protein)] deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation, and alters the methylation of cytosines in DNA. Here, we assess whether the HCHC complex affects genome organization by performing Hi-C in strains deleted of the cdp-2 or chap genes. CDP-2 loss increases intra- and interchromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone PTMs genome-wide, as CDP-2 deletion increases heterochromatic H4K16 acetylation, yet smaller heterochromatic regions lose H3K9 trimethylation and gain interheterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.
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Affiliation(s)
- Ashley W. Scadden
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Alayne S. Graybill
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Clayton Hull-Crew
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Tiffany J. Lundberg
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Nickolas M. Lande
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Andrew D. Klocko
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
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35
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Rogers TF, Simakov O. Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians. Brief Funct Genomics 2023; 22:533-542. [PMID: 37815133 PMCID: PMC10658181 DOI: 10.1093/bfgp/elad043] [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: 04/29/2023] [Revised: 08/17/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023] Open
Abstract
Information on how 3D genome topology emerged in animal evolution, how stable it is during development, its role in the evolution of phenotypic novelties and how exactly it affects gene expression is highly debated. So far, data to address these questions are lacking with the exception of a few key model species. Several gene regulatory mechanisms have been proposed, including scenarios where genome topology has little to no impact on gene expression, and vice versa. The ancient and diverse clade of spiralians may provide a crucial testing ground for such mechanisms. Sprialians have followed distinct evolutionary trajectories, with some clades experiencing genome expansions and/or large-scale genome rearrangements, and others undergoing genome contraction, substantially impacting their size and organisation. These changes have been associated with many phenotypic innovations in this clade. In this review, we describe how emerging genome topology data, along with functional tools, allow for testing these scenarios and discuss their predicted outcomes.
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Affiliation(s)
- Thea F Rogers
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
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36
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Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H. Genome folding principles revealed in condensin-depleted mitotic chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566494. [PMID: 38014261 PMCID: PMC10680603 DOI: 10.1101/2023.11.09.566494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
During mitosis, condensin activity interferes with interphase chromatin structures. Here, we generated condensin-free mitotic chromosomes to investigate genome folding principles. Co-depletion of condensin I and II, but neither alone, triggered mitotic chromosome compartmentalization in ways that differ from interphase. Two distinct euchromatic compartments, indistinguishable in interphase, rapidly emerged upon condensin loss with different interaction preferences and dependence on H3K27ac. Constitutive heterochromatin gradually self-aggregated and co-compartmentalized with the facultative heterochromatin, contrasting with their separation during interphase. While topologically associating domains (TADs) and CTCF/cohesin mediated structural loops remained undetectable, cis-regulatory element contacts became apparent, providing an explanation for their quick re-establishment during mitotic exit. HP1 proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M- to G1-phase in the combined absence of HP1α, HP1β and HP1γ, re-established constitutive heterochromatin compartments normally. In sum, "clean-slate" condensing-deficient mitotic chromosomes illuminate mechanisms of genome compartmentalization not revealed in interphase cells.
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Affiliation(s)
- Han Zhao
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Yinzhi Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - En Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Fuhai Liu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Lirong Shu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Dannan Jing
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Baiyue Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Manzhu Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- School of Basic medicine, Capital Medical University, Beijing, China
| | - Fengnian Shan
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- School of Pharmacology, South China University of Technology, Guangzhou, Guangdong, China
| | - Lin Zhang
- School of Biological Science, Hongkong University, Hongkong, China
| | - Jessica C. Lam
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susannah C. Midla
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Belinda M. Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Gerd A. Blobel
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
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37
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Arias-Sardá C, Quigley S, Farré M. Patterns of chromosome evolution in ruminants. Mol Ecol 2023. [PMID: 37937367 DOI: 10.1111/mec.17197] [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: 06/08/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
Studying when and where gross genomic rearrangements occurred during evolution is key to understanding changes in genome structure with functional consequences that might eventually lead to speciation. Here we identified chromosome rearrangements in ruminants, a clade characterized by large chromosome differences. Using 26 genome assemblies, we reconstructed five ancestral karyotypes and classified the rearrangement events occurring in each lineage. With these reconstructions, we then identified evolutionary breakpoints regions (EBRs) and synteny fragments. Ruminant karyotype evolution is characterized by inversions, while interchromosomal rearrangements occurred preferentially in the oldest ancestor of ruminants. We found that EBRs are depleted of protein coding genes, including housekeeping genes. Similarly, EBRs are not enriched in high GC regions, suggesting that meiotic double strand breaks might not be their origin. Overall, our results characterize at fine detail the location of chromosome rearrangements in ruminant evolution and provide new insights into the formation of EBRs.
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Affiliation(s)
| | - Sarah Quigley
- School of Biosciences, University of Kent, Canterbury, UK
| | - Marta Farré
- School of Biosciences, University of Kent, Canterbury, UK
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38
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Keikhosravi A, Almansour F, Bohrer CH, Fursova NA, Guin K, Sood V, Misteli T, Larson DR, Pegoraro G. HiTIPS: High-Throughput Image Processing Software for the Study of Nuclear Architecture and Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565366. [PMID: 38076967 PMCID: PMC10705580 DOI: 10.1101/2023.11.02.565366] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/14/2024]
Abstract
High-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software for image analysis workflows does not allow full customization and adoption of new image processing algorithms in the analysis modules. While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis modules or algorithms. Here, we introduce the High-Throughput Image Processing Software (HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS incorporates advanced image processing and machine learning algorithms for automated cell and nuclei segmentation, spot signal detection, nucleus tracking, spot tracking, and quantification of spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to integration of new algorithms for existing analysis pipelines and to adding new analysis pipelines through separate plugins. To demonstrate the utility of HiTIPS, we present three examples of image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-friendly, flexible, and open-source HTI analysis platform for a variety of cell biology applications.
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39
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El Yakoubi W, Akera T. Condensin dysfunction is a reproductive isolating barrier in mice. Nature 2023; 623:347-355. [PMID: 37914934 DOI: 10.1038/s41586-023-06700-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 10/02/2023] [Indexed: 11/03/2023]
Abstract
Reproductive isolation occurs when the genomes of two populations accumulate genetic incompatibilities that prevent interbreeding1,2. Understanding of hybrid incompatibility at the cell biology level is limited, particularly in the case of hybrid female sterility3. Here we find that species divergence in condensin regulation and centromere organization between two mouse species, Mus musculus domesticus and Mus spretus, drives chromosome decondensation and mis-segregation in their F1 hybrid oocytes, reducing female fertility. The decondensation in hybrid oocytes was especially prominent at pericentromeric major satellites, which are highly abundant at M. m. domesticus centromeres4-6, leading to species-specific chromosome mis-segregation and egg aneuploidy. Consistent with the condensation defects, a chromosome structure protein complex, condensin II7,8, was reduced on hybrid oocyte chromosomes. We find that the condensin II subunit NCAPG2 was specifically reduced in the nucleus in prophase and that overexpressing NCAPG2 rescued both the decondensation and egg aneuploidy phenotypes. In addition to the overall reduction in condensin II on chromosomes, major satellites further reduced condensin II levels locally, explaining why this region is particularly prone to decondensation. Together, this study provides cell biological insights into hybrid incompatibility in female meiosis and demonstrates that condensin misregulation and pericentromeric satellite expansion can establish a reproductive isolating barrier in mammals.
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Affiliation(s)
- Warif El Yakoubi
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Takashi Akera
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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40
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London N, Medina-Pritchard B, Spanos C, Rappsilber J, Jeyaprakash AA, Allshire RC. Direct recruitment of Mis18 to interphase spindle pole bodies promotes CENP-A chromatin assembly. Curr Biol 2023; 33:4187-4201.e6. [PMID: 37714149 DOI: 10.1016/j.cub.2023.08.063] [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: 06/21/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
CENP-A chromatin specifies mammalian centromere identity, and its chaperone HJURP replenishes CENP-A when recruited by the Mis18 complex (Mis18C) via M18BP1/KNL2 to CENP-C at kinetochores during interphase. However, the Mis18C recruitment mechanism remains unresolved in species lacking M18BP1, such as fission yeast. Fission yeast centromeres cluster at G2 spindle pole bodies (SPBs) when CENP-ACnp1 is replenished and where Mis18C also localizes. We show that SPBs play an unexpected role in concentrating Mis18C near centromeres through the recruitment of Mis18 by direct binding to the major SPB linker of nucleoskeleton and cytoskeleton (LINC) component Sad1. Mis18C recruitment by Sad1 is important for CENP-ACnp1 chromatin establishment and acts in parallel with a CENP-C-mediated Mis18C recruitment pathway to maintain centromeric CENP-ACnp1 but operates independently of Sad1-mediated centromere clustering. SPBs therefore provide a non-chromosomal scaffold for both Mis18C recruitment and centromere clustering during G2. This centromere-independent Mis18-SPB recruitment provides a mechanism that governs de novo CENP-ACnp1 chromatin assembly by the proximity of appropriate sequences to SPBs and highlights how nuclear spatial organization influences centromere identity.
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Affiliation(s)
- Nitobe London
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Bethan Medina-Pritchard
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK; Institute of Biotechnology, Technische Universität, 13355 Berlin, Germany
| | - A Arockia Jeyaprakash
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK; Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Robin C Allshire
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK.
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41
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van Hooff JJE. Towards unraveling the origins of eukaryotic nuclear genome organization. Trends Cell Biol 2023; 33:820-823. [PMID: 37558594 DOI: 10.1016/j.tcb.2023.07.008] [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: 06/01/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023]
Abstract
With 3D genome mapping maturing over the past decade, studies exposed the differences between eukaryotic and prokaryotic genome organization. This raises the question of how the complex eukaryotic genome organization originated. Here, I explore potential pathways to answering this question, guided by our changing understanding of the origins of eukaryotes.
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Affiliation(s)
- Jolien J E van Hooff
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands.
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42
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Sakamoto T, Matsunaga S. Chromatin dynamics and subnuclear gene positioning for transcriptional regulation. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102431. [PMID: 37562088 DOI: 10.1016/j.pbi.2023.102431] [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: 04/08/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023]
Abstract
Plants have been found to exhibit diverse characteristics and functions of chromatin organization, showing both similarities and differences to animals. It is becoming clear how chromatin organization is linked to transcriptional regulation in response to environmental stresses. Regulation of specific chromatin positions in the nuclear space is important for transcription, and the mechanisms that enable such chromatin dynamics are gradually being unveiled. Genes move between subdomains responsible for transcriptional activation or suppression in the subnuclear space in a gene repositioning cycle. We propose a model of localized chromatin interaction in nuclear subdomains, in which the dynamics of local chromatin interactions have a more important impact on the regulation of gene expression than large-scale chromatin organization. In this mini-review, we highlight recent findings on chromatin dynamics, particularly involving transcriptional regulation, and discuss future directions in the study of chromatin organization in plants.
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Affiliation(s)
- Takuya Sakamoto
- Department of Science, Faculty of Science, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-0802, Japan
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
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43
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Scadden AW, Graybill AS, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD. Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547530. [PMID: 37461718 PMCID: PMC10349943 DOI: 10.1101/2023.07.03.547530] [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: 07/25/2023]
Abstract
Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungus Neurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures formed by heterochromatic region aggregation. However, insufficient data exists on how histone post-translational modifications, including acetylation, affect genome organization. In Neurospora, the HCHC complex (comprised of the proteins HDA-1, CDP-2, HP1, and CHAP) deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation and alters the methylation of cytosines in DNA. Here, we assess if the HCHC complex affects genome organization by performing Hi-C in strains deleted of the cdp-2 or chap genes. CDP-2 loss increases intra- and inter-chromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone post-translational modifications genome-wide: without CDP-2, heterochromatic H4K16 acetylation is increased, yet smaller heterochromatic regions lose H3K9 trimethylation and gain inter-heterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder, as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.
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Affiliation(s)
- Ashley W. Scadden
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Alayne S. Graybill
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Clayton Hull-Crew
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Tiffany J. Lundberg
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Nickolas M. Lande
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Andrew D. Klocko
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
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44
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Hristov BH, Noble WS, Bertero A. Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558852. [PMID: 37790381 PMCID: PMC10542540 DOI: 10.1101/2023.09.21.558852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Most studies of genome organization have focused on intra-chromosomal (cis) contacts because they harbor key features such as DNA loops and topologically associating domains. Inter-chromosomal (trans) contacts have received much less attention, and tools for interrogating potential biologically relevant trans structures are lacking. Here, we develop a computational framework to identify sets of loci that jointly interact in trans from Hi-C data. This method, trans-C, initiates probabilistic random walks with restarts from a set of seed loci to traverse an input Hi-C contact network, thereby identifying sets of trans-contacting loci. We validate trans-C in three increasingly complex models of established trans contacts: the Plasmodium falciparum var genes, the mouse olfactory receptor "Greek islands", and the human RBM20 cardiac splicing factory. We then apply trans-C to systematically test the hypothesis that genes co-regulated by the same trans-acting element (i.e., a transcription or splicing factor) co-localize in three dimensions to form "RNA factories" that maximize the efficiency and accuracy of RNA biogenesis. We find that many loci with multiple binding sites of the same transcription factor interact with one another in trans, especially those bound by transcription factors with intrinsically disordered domains. Similarly, clustered binding of a subset of RNA binding proteins correlates with trans interaction of the encoding loci. These findings support the existence of trans interacting chromatin domains (TIDs) driven by RNA biogenesis. Trans-C provides an efficient computational framework for studying these and other types of trans interactions, empowering studies of a poorly understood aspect of genome architecture.
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Affiliation(s)
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
| | - Alessandro Bertero
- Molecular Biotechnology Center “Guido Tarone”, Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy
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45
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Schindler M, Osterwalder M, Harabula I, Wittler L, Tzika AC, Dechmann DKN, Vingron M, Visel A, Haas SA, Real FM. Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes. Development 2023; 150:dev201562. [PMID: 37519269 PMCID: PMC10499028 DOI: 10.1242/dev.201562] [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: 12/30/2022] [Accepted: 07/21/2023] [Indexed: 08/01/2023]
Abstract
Changes in gene expression represent an important source of phenotypic innovation. Yet how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing integrative analyses of epigenetic and transcriptional data in mole and mouse, we identified the co-option of SALL1 expression in mole ovotestes formation. Chromosome conformation capture analyses highlight a striking conservation of the 3D organization at the SALL1 locus, but an evolutionary divergence of enhancer activity. Interspecies reporter assays support the capability of mole-specific enhancers to activate transcription in urogenital tissues. Through overexpression experiments in transgenic mice, we further demonstrate the capability of SALL1 to induce kidney-related gene programs, which are a signature of mole ovotestes. Our results highlight the co-option of gene expression, through changes in enhancer activity, as a plausible mechanism for the evolution of traits.
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Affiliation(s)
- Magdalena Schindler
- Gene Regulation & Evolution, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
- Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Marco Osterwalder
- Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
- Department of Cardiology, Bern University Hospital, Bern 3010, Switzerland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Izabela Harabula
- Epigenetic Regulation and Chromatin Architecture, Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin 10115, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Athanasia C. Tzika
- Department of Genetics & Evolution, University of Geneva, Geneva 1205, Switzerland
| | - Dina K. N. Dechmann
- Department of Migration, Max Planck Institute for Animal Behavior, Radolfzell 78315, Germany
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Stefan A. Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Francisca M. Real
- Gene Regulation & Evolution, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
- Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany
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46
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Abstract
Many cellular processes require large-scale rearrangements of chromatin structure. Structural maintenance of chromosomes (SMC) protein complexes are molecular machines that can provide structure to chromatin. These complexes can connect DNA elements in cis, walk along DNA, build and processively enlarge DNA loops and connect DNA molecules in trans to hold together the sister chromatids. These DNA-shaping abilities place SMC complexes at the heart of many DNA-based processes, including chromosome segregation in mitosis, transcription control and DNA replication, repair and recombination. In this Review, we discuss the latest insights into how SMC complexes such as cohesin, condensin and the SMC5-SMC6 complex shape DNA to direct these fundamental chromosomal processes. We also consider how SMC complexes, by building chromatin loops, can counteract the natural tendency of alike chromatin regions to cluster. SMC complexes thus control nuclear organization by participating in a molecular tug of war that determines the architecture of our genome.
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Affiliation(s)
- Claire Hoencamp
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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47
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Deng L, Zhou Q, Zhou J, Zhang Q, Jia Z, Zhu G, Cheng S, Cheng L, Yin C, Yang C, Shen J, Nie J, Zhu JK, Li G, Zhao L. 3D organization of regulatory elements for transcriptional regulation in Arabidopsis. Genome Biol 2023; 24:181. [PMID: 37550699 PMCID: PMC10405511 DOI: 10.1186/s13059-023-03018-4] [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: 11/19/2022] [Accepted: 07/20/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants. RESULTS Here we perform high-resolution chromatin interaction analysis using paired-end tag sequencing approach. We map chromatin interactions tethered with RNA polymerase II and associated with heterochromatic, transcriptionally active, and Polycomb-repressive histone modifications in Arabidopsis. Analysis of the regulatory repertoire shows that distal active cis-regulatory elements are linked to their target genes through long-range chromatin interactions with increased expression of the target genes, while poised cis-regulatory elements are linked to their target genes through long-range chromatin interactions with depressed expression of the target genes. Furthermore, we demonstrate that transcription factor MYC2 is critical for chromatin spatial organization, and propose that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. Analysis of functionally related gene-defined chromatin connectivity networks reveals that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or Polycomb-repressive mark-associated chromatin conformation to coordinated gene expression. CONCLUSION The results reveal that the regulation of gene transcription in Arabidopsis is not only by linear juxtaposition, but also by long-range chromatin interactions. Our study uncovers the fine scale genome organization of Arabidopsis and the potential roles of such organization in orchestrating transcription and development.
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Affiliation(s)
- Li Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangfeng Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lulu Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Caijun Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junwei Nie
- Vazyme Biotech Co., Ltd., Nanjing, 210000, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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48
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Hehmeyer J, Spitz F, Marlow H. Shifting landscapes: the role of 3D genomic organizations in gene regulatory strategies. Curr Opin Genet Dev 2023; 81:102064. [PMID: 37390583 PMCID: PMC10547022 DOI: 10.1016/j.gde.2023.102064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 07/02/2023]
Abstract
3D genome folding enables the physical storage of chromosomes into the compact volume of a cell's nucleus, allows for the accurate segregation of chromatin to daughter cells, and has been shown to be tightly coupled to the way in which genetic information is converted into transcriptional programs [1-3]. Importantly, this link between chromatin architecture and gene regulation is a selectable feature in which modifications to chromatin organization accompany, or perhaps even drive the establishment of new regulatory strategies with enduring impacts on animal body plan complexity. Here, we discuss the nature of different 3D genome folding systems found across the tree of life, with particular emphasis on metazoans, and the relative influence of these systems on gene regulation. We suggest how the properties of these folding systems have influenced regulatory strategies employed by different lineages and may have catalyzed the partitioning and specialization of genetic programs that enabled multicellularity and organ-grade body plan complexity.
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Affiliation(s)
- Jenks Hehmeyer
- Department of Organismal Biology and Anatomy, The University of Chicago, USA
| | - François Spitz
- Department of Human Genetics, The University of Chicago, USA
| | - Heather Marlow
- Department of Organismal Biology and Anatomy, The University of Chicago, USA.
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Hitz BC, Lee JW, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Strattan JS, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, Ho M, Miyasato S, Simison M, Tanaka F, Luo Y, Whaling I, Hong EL, Lee BT, Sandstrom R, Rynes E, Nelson J, Nishida A, Ingersoll A, Buckley M, Frerker M, Kim DS, Boley N, Trout D, Dobin A, Rahmanian S, Wyman D, Balderrama-Gutierrez G, Reese F, Durand NC, Dudchenko O, Weisz D, Rao SSP, Blackburn A, Gkountaroulis D, Sadr M, Olshansky M, Eliaz Y, Nguyen D, Bochkov I, Shamim MS, Mahajan R, Aiden E, Gingeras T, Heath S, Hirst M, Kent WJ, Kundaje A, Mortazavi A, Wold B, Cherry JM. The ENCODE Uniform Analysis Pipelines. RESEARCH SQUARE 2023:rs.3.rs-3111932. [PMID: 37503119 PMCID: PMC10371165 DOI: 10.21203/rs.3.rs-3111932/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.
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Affiliation(s)
- Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jin-Wook Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meenakshi S Kagda
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keenan Graham
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul Sud
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy Dreszer
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurence D Rowe
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nikhil R Podduturi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Venkat S Malladi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Esther T Chan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcus Ho
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stuart Miyasato
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matt Simison
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Forrest Tanaka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian Whaling
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eurie L Hong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian T Lee
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard Sandstrom
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Andrew Nishida
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Alyssa Ingersoll
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Mark Frerker
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Daniel S Kim
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Nathan Boley
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - Alex Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sorena Rahmanian
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Dana Wyman
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Fairlie Reese
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Neva C Durand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alyssa Blackburn
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Dimos Gkountaroulis
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Mahdi Sadr
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moshe Olshansky
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yossi Eliaz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dat Nguyen
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ivan Bochkov
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad Saad Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Erez Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Tom Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Hirst
- Micheal Smith Laboratories, University of British Columbia, British Columbia, Canada
| | - W James Kent
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anshul Kundaje
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Ali Mortazavi
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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50
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Ma B, Wang H, Liu J, Chen L, Xia X, Wei W, Yang Z, Yuan J, Luo Y, He N. The gap-free genome of mulberry elucidates the architecture and evolution of polycentric chromosomes. HORTICULTURE RESEARCH 2023; 10:uhad111. [PMID: 37786730 PMCID: PMC10541557 DOI: 10.1093/hr/uhad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/15/2023] [Indexed: 10/04/2023]
Abstract
Mulberry is a fundamental component of the global sericulture industry, and its positive impact on our health and the environment cannot be overstated. However, the mulberry reference genomes reported previously remained unassembled or unplaced sequences. Here, we report the assembly and analysis of the telomere-to-telomere gap-free reference genome of the mulberry species, Morus notabilis, which has emerged as an important reference in mulberry gene function research and genetic improvement. The mulberry gap-free reference genome produced here provides an unprecedented opportunity for us to study the structure and function of centromeres. Our results revealed that all mulberry centromeric regions share conserved centromeric satellite repeats with different copies. Strikingly, we found that M. notabilis is a species with polycentric chromosomes and the only reported polycentric chromosome species up to now. We propose a compelling model that explains the formation mechanism of new centromeres and addresses the unsolved scientific question of the chromosome fusion-fission cycle in mulberry species. Our study sheds light on the functional genomics, chromosome evolution, and genetic improvement of mulberry species.
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Affiliation(s)
- Bi Ma
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Honghong Wang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Jingchun Liu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Lin Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Xiaoyu Xia
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Wuqi Wei
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Zhen Yang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Jianglian Yuan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Yiwei Luo
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Ningjia He
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
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