1
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Zheng S, Thakkar N, Harris HL, Liu S, Zhang M, Gerstein M, Aiden EL, Rowley MJ, Noble WS, Gürsoy G, Singh R. Predicting A/B compartments from histone modifications using deep learning. iScience 2024; 27:109570. [PMID: 38646172 PMCID: PMC11031843 DOI: 10.1016/j.isci.2024.109570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 04/23/2024] Open
Abstract
The three-dimensional organization of genomes plays a crucial role in essential biological processes. The segregation of chromatin into A and B compartments highlights regions of activity and inactivity, providing a window into the genomic activities specific to each cell type. Yet, the steep costs associated with acquiring Hi-C data, necessary for studying this compartmentalization across various cell types, pose a significant barrier in studying cell type specific genome organization. To address this, we present a prediction tool called compartment prediction using recurrent neural networks (CoRNN), which predicts compartmentalization of 3D genome using histone modification enrichment. CoRNN demonstrates robust cross-cell-type prediction of A/B compartments with an average AuROC of 90.9%. Cell-type-specific predictions align well with known functional elements, with H3K27ac and H3K36me3 identified as highly predictive histone marks. We further investigate our mispredictions and found that they are located in regions with ambiguous compartmental status. Furthermore, our model's generalizability is validated by predicting compartments in independent tissue samples, which underscores its broad applicability.
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Affiliation(s)
- Suchen Zheng
- Department of Computer Science, Brown University, Providence, RI, USA
| | - Nitya Thakkar
- Department of Computer Science, Brown University, Providence, RI, USA
| | - Hannah L. Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Susanna Liu
- Data Science and Statistics, Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Megan Zhang
- Data Science and Statistics, Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics, Molecular Biophysics & Biochemistry, Data Science and Statistics, Computer Science, Yale University, New Haven, CT, USA
| | - Erez Lieberman Aiden
- Department of Genetics, Baylor College of Medicine, Department of Computer Science, Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - M. Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - William Stafford Noble
- Department of Genome Sciences, Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Gamze Gürsoy
- Department of Biomedical Informatics, Columbia University, New York Genome Center, New York, NY, USA
| | - Ritambhara Singh
- Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA
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2
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Keller D, Stinus S, Umlauf D, Gourbeyre E, Biot E, Olivier N, Mahou P, Beaurepaire E, Andrey P, Crabbe L. Non-random spatial organization of telomeres varies during the cell cycle and requires LAP2 and BAF. iScience 2024; 27:109343. [PMID: 38510147 PMCID: PMC10951912 DOI: 10.1016/j.isci.2024.109343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Spatial genome organization within the nucleus influences major biological processes and is impacted by the configuration of linear chromosomes. Here, we applied 3D spatial statistics and modeling on high-resolution telomere and centromere 3D-structured illumination microscopy images in cancer cells. We found a multi-scale organization of telomeres that dynamically evolved from a mixed clustered-and-regular distribution in early G1 to a purely regular distribution as cells progressed through the cell cycle. In parallel, our analysis revealed two pools of peripheral and internal telomeres, the proportions of which were inverted during the cell cycle. We then conducted a targeted screen using MadID to identify the molecular pathways driving or maintaining telomere anchoring to the nuclear envelope observed in early G1. Lamina-associated polypeptide (LAP) proteins were found transiently localized to telomeres in anaphase, a stage where LAP2α initiates the reformation of the nuclear envelope, and impacted telomere redistribution in the next interphase together with their partner barrier-to-autointegration factor (BAF).
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Affiliation(s)
- Debora Keller
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Sonia Stinus
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - David Umlauf
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Edith Gourbeyre
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Eric Biot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Nicolas Olivier
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Philippe Andrey
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Laure Crabbe
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
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3
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Islam A, Manjarrez-González JC, Song X, Gore T, Draviam VM. Search for chromosomal instability aiding variants reveal naturally occurring kinetochore gene variants that perturb chromosome segregation. iScience 2024; 27:109007. [PMID: 38361632 PMCID: PMC10867425 DOI: 10.1016/j.isci.2024.109007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/15/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancers, and CIN-promoting mutations are not fully understood. Here, we report 141 chromosomal instability aiding variant (CIVa) candidates by assessing the prevalence of loss-of-function (LoF) variants in 135 chromosome segregation genes from over 150,000 humans. Unexpectedly, we observe both heterozygous and homozygous CIVa in Astrin and SKA3, two evolutionarily conserved kinetochore and microtubule-associated proteins essential for chromosome segregation. To stratify harmful versus harmless variants, we combine live-cell microscopy and controlled protein expression. We find the naturally occurring Astrin p.Q1012∗ variant is harmful as it fails to localize normally and induces chromosome misalignment and missegregation, in a dominant negative manner. In contrast, the Astrin p.L7Qfs∗21 variant generates a shorter isoform that localizes and functions normally, and the SKA3 p.Q70Kfs∗7 variant allows wild-type SKA complex localisation and function, revealing distinct resilience mechanisms that render these variants harmless. Thus, we present a scalable framework to predict and stratify naturally occurring CIVa, and provide insight into resilience mechanisms that compensate for naturally occurring CIVa.
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Affiliation(s)
- Asifa Islam
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | | | - Xinhong Song
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Trupti Gore
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
- London Interdisciplinary Doctoral Program, University College London, London, UK
| | - Viji M. Draviam
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
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4
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Paturej J, Erbas A. Cyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization. Phys Biol 2023. [PMID: 37442118 DOI: 10.1088/1478-3975/ace750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Interphase chromosomes are known to organize non-randomly in the micron-sized eukaryotic cell nucleus and occupy certain fraction of nuclear volume, often without mixing. Using extensive coarse-grained simulations, we model such chromosome structures as colloidal particles whose surfaces are grafted by cyclic polymers. This model system is known as Rosetta. The cyclic polymers, with varying polymerization degrees, mimic chromatin loops present in interphase chromosomes, while the rigid core models the chromocenter section of the chromosome. Our simulations show that the colloidal chromosome model provides a well-separated particle distribution without specific attraction between the chain monomers. As the polymerization degree of the grafted cyclic chains decreases while maintaining the total chromosomal length (e.g., the more potent activity of condensin-family proteins), the average chromosomal volume becomes smaller, inter-chromosomal contacts decrease, and chromocenters organize in a quasi-crystalline order reminiscent of a glassy state. This order weakens for polymer chains with a characteristic size on the order of the confinement radius. Notably, linear-polymer grafted particles also provide the same chromocenter organization scheme. However, unlike linear chains, cyclic chains result in less contact between the polymer layers of neighboring chromosome particles, demonstrating the effect of DNA breaks in altering genome-wide contacts. Our simulations show that polymer-grafted colloidal systems could help decipher 3D genome architecture along with the fractal globular and loop-extrusion models.
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Affiliation(s)
- Jaroslaw Paturej
- Institute of Physics, University of Silesia, Katowice, Katowice, 40-007, POLAND
| | - Aykut Erbas
- Bilkent University, 06800 Ankara, Ankara, 06800, TURKEY
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5
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Yamamoto K, Matsuzaki R, Mahakham W, Heman W, Sekimoto H, Kawachi M, Minakuchi Y, Toyoda A, Nozaki H. Expanded male sex-determining region conserved during the evolution of homothallism in the green alga Volvox. iScience 2023; 26:106893. [PMID: 37378338 PMCID: PMC10291315 DOI: 10.1016/j.isci.2023.106893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
Male and female genotypes in heterothallic (self-incompatible) species of haploid organisms, such as algae and bryophytes, are generally determined by male and female sex-determining regions (SDRs) in the sex chromosomes. To resolve the molecular genetic basis for the evolution of homothallic (bisexual and self-compatible) species from a heterothallic ancestor, we compared whole-genome data from Thai and Japanese genotypes within the homothallic green alga Volvox africanus. The Thai and Japanese algae harbored expanded ancestral male and female SDRs of ∼1 Mbp each, representing a direct heterothallic ancestor. Therefore, the expanded male and female ancestral SDRs may originate from the ancient (∼75 mya) heterothallic ancestor, and either might have been conserved during the evolution of each homothallic genotype. An expanded SDR-like region seems essential for homothallic sexual reproduction in V. africanus, irrespective of male or female origin. Our study stimulates future studies to elucidate the biological significance of such expanded genomic regions.
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Affiliation(s)
- Kayoko Yamamoto
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University, Tokyo 112-8681 Japan
| | - Ryo Matsuzaki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Wuttipong Mahakham
- Department of Biology & Applied Taxonomic Research Center, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Wirawan Heman
- Department of Science and Mathematics, Faculty of Science and Health Technology, Kalasin University, Mueang Kalasin, Thailand
| | - Hiroyuki Sekimoto
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University, Tokyo 112-8681 Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Yohei Minakuchi
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima 411-8540, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima 411-8540, Japan
| | - Hisayoshi Nozaki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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6
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Abstract
Structural maintenance of chromosomes (SMC) complexes guard and organize the three-dimensional structure of chromosomal DNA across the tree of life. Many SMC functions can be explained by an inherent motor activity that extrudes large DNA loops while the complexes move along their substrate. Here, we review recent structural insights into the architecture and conservation of these molecular machines, their interaction with DNA, and the conformational changes that are linked to their ATP hydrolysis cycle.
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Affiliation(s)
- Frank Bürmann
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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7
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Sundararajan S, Park H, Kawano S, Johansson M, Lama B, Saito-Fujita T, Saitoh N, Arnaoutov A, Dasso M, Wang Z, Keifenheim D, Clarke DJ, Azuma Y. Methylated histones on mitotic chromosomes promote topoisomerase IIα function for high fidelity chromosome segregation. iScience 2023; 26:106743. [PMID: 37197327 PMCID: PMC10183659 DOI: 10.1016/j.isci.2023.106743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/31/2022] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
DNA Topoisomerase IIα (TopoIIα) decatenates sister chromatids, allowing their segregation in mitosis. Without the TopoIIα Strand Passage Reaction (SPR), chromosome bridges and ultra-fine DNA bridges (UFBs) arise in anaphase. The TopoIIα C-terminal domain is dispensable for the SPR in vitro but essential for mitotic functions in vivo. Here, we present evidence that the Chromatin Tether (ChT) within the CTD interacts with specific methylated nucleosomes and is crucial for high-fidelity chromosome segregation. Mutation of individual αChT residues disrupts αChT-nucleosome interaction, induces loss of segregation fidelity and reduces association of TopoIIα with chromosomes. Specific methyltransferase inhibitors reducing histone H3 or H4 methylation decreased TopoIIα at centromeres and increased segregation errors. Methyltransferase inhibition did not further increase aberrant anaphases in the ChT mutants, indicating a functional connection. The evidence reveals novel cellular regulation whereby TopoIIα specifically interacts with methylated nucleosomes via the αChT to ensure high-fidelity chromosome segregation.
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Affiliation(s)
- Sanjana Sundararajan
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Hyewon Park
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Shinji Kawano
- Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0081, Japan
| | - Marnie Johansson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bunu Lama
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Tomoko Saito-Fujita
- Division of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Alexei Arnaoutov
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-4480, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-4480, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel Keifenheim
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Duncan J. Clarke
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Corresponding author
| | - Yoshiaki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
- Corresponding author
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8
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Moreno SP, Fusté JM, Kaiser M, Li JSZ, Nassour J, Haggblom C, Denchi EL, Karlseder J. TZAP overexpression induces telomere dysfunction and ALT-like activity in ATRX/DAXX-deficient cells. iScience 2023; 26:106405. [PMID: 37013192 PMCID: PMC10066556 DOI: 10.1016/j.isci.2023.106405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/13/2022] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
The appropriate regulation of telomere length homeostasis is crucial for the maintenance of genome integrity. The telomere-binding protein TZAP has been suggested to regulate telomere length by promoting t-circle and c-circle excisions through telomere trimming, yet the molecular mechanisms by which TZAP functions at telomeres are not understood. Using a system based on TZAP overexpression, we show that efficient TZAP recruitment to telomeres occurs in the context of open telomeric chromatin caused by loss of ATRX/DAXX independently of H3.3 deposition. Moreover, our data indicate that TZAP binding to telomeres induces telomere dysfunction and ALT-like activity, resulting in the generation of t-circles and c-circles in a Bloom-Topoisomerase IIIα-RMI1-RMI2 (BTR)-dependent manner.
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Affiliation(s)
- Sara Priego Moreno
- The Salk Institute for Biological Studies, Molecular and Cell Biology Department, 10010 N. Torrey pines Road, La Jolla, CA 92037, USA
| | - Javier Miralles Fusté
- The Salk Institute for Biological Studies, Molecular and Cell Biology Department, 10010 N. Torrey pines Road, La Jolla, CA 92037, USA
| | - Melanie Kaiser
- The Salk Institute for Biological Studies, Molecular and Cell Biology Department, 10010 N. Torrey pines Road, La Jolla, CA 92037, USA
| | - Julia Su Zhou Li
- The Ludwig Institute for Cancer Research, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joe Nassour
- The Salk Institute for Biological Studies, Molecular and Cell Biology Department, 10010 N. Torrey pines Road, La Jolla, CA 92037, USA
| | - Candy Haggblom
- The Salk Institute for Biological Studies, Molecular and Cell Biology Department, 10010 N. Torrey pines Road, La Jolla, CA 92037, USA
| | - Eros Lazzerini Denchi
- Laboratory for Genome Integrity, National Cancer Institute, Building 37, Room 2144B, Bethesda, MD 20892, USA
| | - Jan Karlseder
- The Salk Institute for Biological Studies, Molecular and Cell Biology Department, 10010 N. Torrey pines Road, La Jolla, CA 92037, USA
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9
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Shah R, Gallardo CM, Jung YH, Clock B, Dixon JR, McFadden WM, Majumder K, Pintel DJ, Corces VG, Torbett BE, Tedbury PR, Sarafianos SG. Activation of HIV-1 proviruses increases downstream chromatin accessibility. iScience 2022; 25:105490. [PMID: 36505924 PMCID: PMC9732416 DOI: 10.1016/j.isci.2022.105490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
It is unclear how the activation of HIV-1 transcription affects chromatin structure. We interrogated chromatin organization both genome-wide and nearby HIV-1 integration sites using Hi-C and ATAC-seq. In conjunction, we analyzed the transcription of the HIV-1 genome and neighboring genes. We found that long-range chromatin contacts did not differ significantly between uninfected cells and those harboring an integrated HIV-1 genome, whether the HIV-1 genome was actively transcribed or inactive. Instead, the activation of HIV-1 transcription changes chromatin accessibility immediately downstream of the provirus, demonstrating that HIV-1 can alter local cellular chromatin structure. Finally, we examined HIV-1 and neighboring host gene transcripts with long-read sequencing and found populations of chimeric RNAs both virus-to-host and host-to-virus. Thus, multiomics profiling revealed that the activation of HIV-1 transcription led to local changes in chromatin organization and altered the expression of neighboring host genes.
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Affiliation(s)
- Raven Shah
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Christian M. Gallardo
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Yoonhee H. Jung
- Department of Biology, Emory University, Atlanta, GA 30329, USA
| | - Ben Clock
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jesse R. Dixon
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - William M. McFadden
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Kinjal Majumder
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David J. Pintel
- Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | | | - Bruce E. Torbett
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
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10
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Yang JY, Chang JM. Pattern recognition of topologically associating domains using deep learning. BMC Bioinformatics 2022; 22:634. [PMID: 36482308 PMCID: PMC9732975 DOI: 10.1186/s12859-022-05075-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have been shown to be a chromosomal structural unit. During evolution, these are conserved based on checking synteny block cross species. Are there common TAD patterns across species or cell lines? RESULTS To address the above question, we propose a novel task-TAD recognition-as opposed to traditional TAD identification. Specifically, we treat Hi-C maps as images, thus re-casting TAD recognition as image pattern recognition, for which we use a convolutional neural network and a residual neural network. In addition, we propose an elegant way to generate non-TAD data for binary classification. We demonstrate deep learning performance which is quite promising, AUC > 0.80, through cross-species and cell-type validation. CONCLUSIONS TADs have been shown to be conserved during evolution. Interestingly, our results confirm that the TAD recognition model is practical across species, which indicates that TADs between human and mouse show common patterns from an image classification point of view. Our approach could be a new way to identify TAD variations or patterns among Hi-C maps. For example, TADs of two Hi-C maps are conserved if the two classification models are exchangeable.
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Affiliation(s)
- Jhen Yuan Yang
- grid.412042.10000 0001 2106 6277Department of Computer Science, National Chengchi University, 11605 Taipei City, Taiwan
| | - Jia-Ming Chang
- grid.412042.10000 0001 2106 6277Department of Computer Science, National Chengchi University, 11605 Taipei City, Taiwan
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11
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Hsia CR, McAllister J, Hasan O, Judd J, Lee S, Agrawal R, Chang CY, Soloway P, Lammerding J. Confined migration induces heterochromatin formation and alters chromatin accessibility. iScience 2022; 25:104978. [PMID: 36117991 PMCID: PMC9474860 DOI: 10.1016/j.isci.2022.104978] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 01/17/2023] Open
Abstract
During migration, cells often squeeze through small constrictions, requiring extensive deformation. We hypothesized that nuclear deformation associated with such confined migration could alter chromatin organization and function. By studying cells migrating through microfluidic devices that mimic interstitial spaces in vivo, we found that confined migration results in increased H3K9me3 and H3K27me3 heterochromatin marks that persist for days. This "confined migration-induced heterochromatin" (CMiH) was distinct from heterochromatin formation during migration initiation. Confined migration decreased chromatin accessibility at intergenic regions near centromeres and telomeres, suggesting heterochromatin spreading from existing sites. Consistent with the overall decrease in accessibility, global transcription was decreased during confined migration. Intriguingly, we also identified increased accessibility at promoter regions of genes linked to chromatin silencing, tumor invasion, and DNA damage response. Inhibiting CMiH reduced migration speed, suggesting that CMiH promotes confined migration. Together, our findings indicate that confined migration induces chromatin changes that regulate cell migration and other functions.
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Affiliation(s)
- Chieh-Ren Hsia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA,Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jawuanna McAllister
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ovais Hasan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seoyeon Lee
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA,Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Richa Agrawal
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chao-Yuan Chang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA,Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Paul Soloway
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA,Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA,Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA,Corresponding author
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12
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Jost D. Polymer Modeling of 3D Epigenome Folding: Application to Drosophila. Methods Mol Biol 2022; 2301:293-305. [PMID: 34415542 DOI: 10.1007/978-1-0716-1390-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mechanistic modeling in biology allows to investigate, based on first principles, if putative hypotheses are compatible with observations and to drive further experimental works. Along this line, polymer modeling has been instrumental in 3D genomics to better understand the impact of key mechanisms on the spatial genome organization. Here, I describe how polymer-based models can be practically used to study the role of epigenome in chromosome folding. I illustrate this methodology in the context of Drosophila epigenome folding.
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Affiliation(s)
- Daniel Jost
- University of Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France.
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13
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Abstract
Over the last decade, genomic proximity ligation approaches have reshaped our vision of chromosomes 3D organizations, from bacteria nucleoids to larger eukaryotic genomes. The different protocols (3Cseq, Hi-C, TCC, MicroC [XL], Hi-CO, etc.) rely on common steps (chemical fixation digestion, ligation…) to detect pairs of genomic positions in close proximity. The most common way to represent these data is a matrix, or contact map, which allows visualizing the different chromatin structures (compartments, loops, etc.) that can be associated to other signals such as transcription, protein occupancy, etc. as well as, in some instances, to biological functions.In this chapter we present and discuss the filtering of the events recovered in proximity ligation experiments as well as the application of the balancing normalization procedure on the resulting contact map. We also describe a computational tool for visualizing normalized contact data dubbed Scalogram.The different processes described here are illustrated and supported by the laboratory custom-made scripts pooled into "hicstuff," an open-access python package accessible on github ( https://github.com/koszullab/hicstuff ).
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Affiliation(s)
- Cyril Matthey-Doret
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Shogofa Mortaza
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Pierrick Moreau
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Axel Cournac
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France.
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14
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Badrinarayanan A, Leake MC. Fluorescence Recovery After Photobleaching (FRAP) to Study Dynamics of the Structural Maintenance of Chromosome (SMC) Complex in Live Escherichia coli Bacteria. Methods Mol Biol 2022; 2476:31-41. [PMID: 35635695 DOI: 10.1007/978-1-0716-2221-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
MukBEF, a structural maintenance of chromosome (SMC) complex, is an important molecular machine for chromosome organization and segregation in Escherichia coli. Fluorescently tagged MukBEF forms distinct spots (or "foci") composed of molecular assemblies in the cell, where it is thought to carry out most of its chromosome-associated activities. Here, we outline the technique of fluorescence recovery after photobleaching (FRAP) as a method to study the properties of YFP-tagged MukB in fluorescent foci. This method can provide important insight into the dynamics of MukB on DNA and be used to study its biochemical properties in vivo.
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Affiliation(s)
| | - Mark C Leake
- Departments of Physics and Biology, University of York, York, UK
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15
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Rosa A. The Physical Behavior of Interphase Chromosomes: Polymer Theory and Coarse-Grain Computer Simulations. Methods Mol Biol 2022; 2301:235-58. [PMID: 34415539 DOI: 10.1007/978-1-0716-1390-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fluorescence in situ hybridization and chromosome conformation capture methods point to the same conclusion: that chromosomes appear to the external observer as compact structures with a highly nonrandom three-dimensional organization. In this work, we recapitulate the efforts made by us and other groups to rationalize this behavior in terms of the mathematical language and tools of polymer physics. After a brief introduction dedicated to some crucial experiments dissecting the structure of interphase chromosomes, we discuss at a nonspecialistic level some fundamental aspects of theoretical and numerical polymer physics. Then, we inglobe biological and polymer aspects into a polymer model for interphase chromosomes which moves from the observation that mutual topological constraints, such as those typically present between polymer chains in ordinary melts, induce slow chain dynamics and "constraint" chromosomes to resemble double-folded randomly branched polymer conformations. By explicitly turning these ideas into a multi-scale numerical algorithm which is described here in full details, we can design accurate model polymer conformations for interphase chromosomes and offer them for systematic comparison to experiments. The review is concluded by discussing the limitations of our approach and pointing to promising perspectives for future work.
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16
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Liao X, Guo S, Yin X, Liao B, Li M, Su H, Li Q, Pei J, Gao J, Lei J, Li X, Huang Z, Xu J, Chen S. Hierarchical chromatin features reveal the toxin production in Bungarus multicinctus. Chin Med 2021; 16:90. [PMID: 34535171 PMCID: PMC8447776 DOI: 10.1186/s13020-021-00502-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bungarus multicinctus, from which a classical Chinese medicine is produced, is known as the most venomous land snake in the world, but the chromatin organization and transcription factor activity during venom replenishment progress have not been explored yet. This study aimed to determine the roles of chromatin structure in toxin activity via bioinformatics and experimental validation. METHODS Chromosome conformation capture (Hi-C) analysis was used to examine interactions among chromosomes and identify different scales of chromatin during envenomation in B. multicinctus. Correlations between epigenetic modifications and chromatin structure were verified through ChIP-seq analysis. RNA-seq was used to validate the influence of variation in chromatin structure and gene expression levels on venom production and regulation. RESULTS Our results suggested that intra-chromosomal interactions are more intense than inter-chromosomal interactions among the control group, 3-day group of venom glands and muscles. Through this, we found that compartmental transition was correlated with chromatin interactions. Interestingly, the up-regulated genes in more compartmental switch regions reflect the function of toxin activity. Topologically associated domain (TAD) boundaries enriched with histone modifications are associated with different distributions of genes and the expression levels. Toxin-coding genes in the same loop are highly expressed, implying that the importance of epigenetic regulation during envenomination. On a smaller scale, the epigenetic markers affect transcriptional regulation by controlling the recruitment/inhibition of transcription initiation complexes. CONCLUSIONS Chromatin structure and epigenetic modifications could play a vital status role in the mechanisms of venom regulation in B. multicinctus.
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Affiliation(s)
- Xuejiao Liao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shuai Guo
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xianmei Yin
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Mingqian Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - He Su
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510006, China
| | - Qiushi Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jihai Gao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Juan Lei
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhihai Huang
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510006, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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17
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de Castro IJ, Toner B, Xie SQ, Swingland J, Hodges A, Tabrizi SJ, Turkheimer F, Pombo A, Khalil A. Altered nuclear architecture in blood cells from Huntington's disease patients. Neurol Sci 2021; 43:379-385. [PMID: 33974169 DOI: 10.1007/s10072-021-05289-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/26/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Cell nuclear architecture has been explored in cancer and laminopathies but not in neurodegenerative disorders. Huntington's disease (HD) is a neurodegenerative disorder that leads to neuronal death. Chromosome-wide changes in gene expression have been reported in HD, not only in the brain but also in peripheral blood cells, but whether this translates into nuclear and chromosome architecture alterations has not yet been studied. METHODS We investigate nuclear structure and chromosome organization in HD blood cells using fluorescence in situ hybridization in ultrathin cryosections (cryoFISH), coupled with machine learning image analysis to evaluate size, distribution, and morphology of nuclei and chromosomes. Four chromosomes were analyzed based on up- or downregulation of gene expression in HD. RESULTS We show that blood cells from HD patients display increased nuclear size and filamentary shape, increased size of gene-rich chromosome 19, decreased filamentary shape of gene-rich chromosome 22, and a more radially centralized position for chromosome 19, whereas chromosomes 4 and 5 do not show detectable differences. CONCLUSIONS We identify gross changes in nuclear architecture and chromosome organization associated with HD in blood. This adds a new layer of information onto disrupting mechanisms in HD and increases the potential of using blood to survey HD.
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Affiliation(s)
- Inês J de Castro
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK. .,Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany. .,Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, Im Neuenheimer Feld 344, Heidelberg, 69120, Germany.
| | - Brian Toner
- CompuMAINE Lab, Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA
| | - Sheila Q Xie
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK.,Chromatin and Development Group, MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - James Swingland
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK.,GRIP AI, London, EC2A 3AZ, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Angela Hodges
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Sarah J Tabrizi
- UCL Institute of Neurology, Box 104, National Hospital for Neurology and Neurosurgery Queen Square, University College London, London, WC1N 3BG, UK
| | - Federico Turkheimer
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK.,Huntington's Disease Centre, Department of Neurodegenerative Disease, University College London (UCL) Queen Square Institute of Neurology and the UK Dementia Research Institute, UCL, London, UK
| | - Ana Pombo
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK.,Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - André Khalil
- CompuMAINE Lab, Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA.
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18
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Ivanova NG, Ostromyshenskii D, Podgornaya O. Tandem Repeat-Based Probes Support the Loop Model of Pericentromere Packing. Cytogenet Genome Res 2021; 161:93-102. [PMID: 33601374 DOI: 10.1159/000513228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/18/2020] [Indexed: 11/19/2022] Open
Abstract
Constitutive heterochromatin is the most mysterious part of the eukaryotic genome. It forms vital chromosome regions such as the centromeric and the pericentromeric ones. The main component of heterochromatic regions are tandem repeats (TR), and their specific organization complicates assembly, annotation, and mapping of these regions. Unannotated and unmapped TR arrays are still present in database contigs. In this study, we used a set of TR in the genomes of the pig (Sus scrofa) and the Chinese hamster (Cricetulus griseus) identified with the help of bioinformatics techniques and determined the specificity of the designed probes. The signal of the 4 pig TR probes in spermatogenic cells was often ring-shaped, especially in primary spermatocytes. The rings were located in the regions relatively weakly stained with DAPI. The unique assembly of the centromeric region was traced using the hamster meiotic chromosomes. The probe specific to chromosome 5 was used. Two signals, arranged as rings, were seen at the pachytene stage, similar to those in the pig spermatogenic cells. In the spermatogenic cells of both pig and hamster, the rings appeared on the chromosomes with pericentromeric TR probes. Our observations support the loop model of the centromeric region, the size of the loops being about 50 kb.
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Affiliation(s)
- Nadezhda G Ivanova
- Laboratory of Non-coding DNA, Institute of Cytology RAS, St. Petersburg, Russian Federation,
| | | | - Olga Podgornaya
- Laboratory of Non-coding DNA, Institute of Cytology RAS, St. Petersburg, Russian Federation.,Department of Cytology and Histology, St. Petersburg State University, St. Petersburg, Russian Federation
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19
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Peng AYT, Kolhe JA, Behrens LD, Freeman BC. Genome organization: Tag it, move it, place it. Curr Opin Cell Biol 2020; 68:90-97. [PMID: 33166737 DOI: 10.1016/j.ceb.2020.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/28/2020] [Accepted: 10/08/2020] [Indexed: 12/14/2022]
Abstract
Chromosomes are selectively organized within the nuclei of interphase cells reflecting the current fate of each cell and are reorganized in response to various physiological cues to maintain homeostasis. Although substantial progress is being made to establish the various patterns of genome architecture, less is understood on how chromosome folding/positioning is achieved. Here, we discuss recent insights into the cellular mechanisms dictating chromatin movements including the use of epigenetic modifications and allosterically regulated transcription factors, as well as a nucleoskeleton system comprised of actin, myosin, and actin-binding proteins. Together, these nuclear factors help coordinate the positioning of both general and cell-specific genomic architectural features.
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Affiliation(s)
- Audrey Yi Tyan Peng
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA
| | - Janhavi A Kolhe
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA
| | - Lindsey D Behrens
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA
| | - Brian C Freeman
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA.
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20
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Mäkelä J, Sherratt D. SMC complexes organize the bacterial chromosome by lengthwise compaction. Curr Genet 2020; 66:895-9. [PMID: 32300862 DOI: 10.1007/s00294-020-01076-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 11/13/2022]
Abstract
Structural maintenance of chromosomes (SMC) complexes are ancient and conserved molecular machines that organize chromosomes in all domains of life. We propose that the principles of chromosome folding needed to accommodate DNA inside a cell in an accessible form will follow similar principles in prokaryotes and eukaryotes. However, the exact contributions of SMC complexes to bacterial chromosome organization have been elusive. Recently, it was shown that the SMC homolog, MukBEF, organizes and individualizes the Escherichia coli chromosome by forming a filamentous axial core from which DNA loops emanate, similar to the action of condensin in mitotic chromosome formation. MukBEF action, along with its interaction with the partner protein, MatP, also facilitates chromosome individualization by directing opposite chromosome arms (replichores) to different cell halves. This contrasts with the situation in many other bacteria, where SMC complexes organise chromosomes in a way that the opposite replichores are aligned along the long axis of the cell. We highlight the similarities and differences of SMC complex contributions to chromosome organization in bacteria and eukaryotes, and summarize the current mechanistic understanding of the processes.
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21
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Drosopoulou E, Gariou-Papalexiou A, Karamoustou E, Gouvi G, Augustinos AA, Bourtzis K, Zacharopoulou A. The chromosomes of Drosophila suzukii (Diptera: Drosophilidae): detailed photographic polytene chromosomal maps and in situ hybridization data. Mol Genet Genomics 2019; 294:1535-46. [PMID: 31346719 DOI: 10.1007/s00438-019-01595-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/15/2019] [Indexed: 01/25/2023]
Abstract
The spotted wing drosophila, D. suzukii, is a serious agricultural pest attacking a variety of soft fruits and vegetables. Although originating from East Asia it has recently invaded America and Europe raising major concern about its expansion potential and the consequent economic losses. Since cytogenetic information on the species is scarce, we report here the mitotic karyotype and detailed photographic maps of the salivary gland polytene chromosomes of D. suzukii. The mitotic metaphase complement contains three pairs of autosomes, one of which is dot-like, and one pair of heteromorphic (XX/XY) sex chromosomes. The salivary gland polytene complement consists of five long polytene arms, representing the two metacentric autosomes and the acrocentric X chromosome, and one very short polytene element, which corresponds to the dot-like autosome. Banding pattern as well as the most characteristic features and prominent landmarks of each polytene chromosome arm are presented and discussed. Furthermore, twelve gene markers have been mapped on the polytene chromosomes of D. suzukii by in situ hybridization. Their distribution pattern was found quite similar to that of D. melanogaster revealing conservation of synteny although the relative position within each chromosome arm for most of the genes differed significantly between D. suzukii and D. melanogaster. The chromosome information presented here is suitable for comparative cytogenetic studies and phylogenetic exploration, while it could also facilitate the assembly of the genome sequence and support the development of genetic tools for species-specific and environment-friendly biological control applications such as the sterile insect technique.
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22
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Lin JL, Ekas H, Deaner M, Alper HS. CRISPR-PIN: Modifying gene position in the nucleus via dCas9-mediated tethering. Synth Syst Biotechnol 2019; 4:73-78. [PMID: 30820479 PMCID: PMC6378893 DOI: 10.1016/j.synbio.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/18/2019] [Accepted: 02/11/2019] [Indexed: 01/24/2023] Open
Abstract
Spatial organization of DNA within the nucleus is important for controlling DNA replication and repair, genetic recombination, and gene expression. Here, we present CRISPR-PIN, a CRISPR/dCas9-based tool that allows control of gene Position in the Nucleus for the yeast Saccharomyces cerevisiae. This approach utilizes a cohesin-dockerin interaction between dCas9 and a perinuclear protein. In doing so, we demonstrate that a single gRNA can enable programmable interaction of nuclear DNA with the nuclear periphery. We demonstrate the utility of this approach for two applications: the controlled segregation of an acentric plasmid and the re-localization of five endogenous loci. In both cases, we obtain results on par with prior reports using traditional, more cumbersome genetic systems. Thus, CRISPR-PIN offers the opportunity for future studies of chromosome biology and gene localization. dCas9 artificially localized to nuclear periphery using cohesin-dockerin tether to ESC1. Targeting dCas9 to acentric plasmid allows rescue of plasmid segregation phenotype. 5 unique chromosomal loci re-localized to nuclear periphery. dCas9 tethering allows control over target gene Position In the Nucleus (CRISPR-PIN).
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Affiliation(s)
- Jyun-Liang Lin
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Holly Ekas
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Matthew Deaner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
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23
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Gong W, Liu Y, Qu H, Liu A, Sun P, Wang X. The effect of CTCF binding sites destruction by CRISPR/Cas9 on transcription of metallothionein gene family in liver hepatocellular carcinoma. Biochem Biophys Res Commun 2019; 510:530-538. [PMID: 30738580 DOI: 10.1016/j.bbrc.2019.01.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 01/24/2019] [Indexed: 01/20/2023]
Abstract
Chromatin spatial organization is essential for transcriptional modulation and stabilization. The pattern of DNA distal interplay form the multiple topological associating domains (TADs), and further assemble the functional compartmentalization with open and expression-active chromatin ("A" compartments) or closed and expression-inactive chromatin ("B" compartments) in genome, whose boundaries were defined by the high enrichment of CCCTC-binding factor (CTCF). Nevertheless, As a potential therapeutic strategy, changing the local chromatin architecture via adding or removing the CTCF binding sites in situ to regulate the transcription activity of genes within one TAD in cancer cells is poorly explored. In present study, we observed that the metallothionein (MT) family were all remarkably decreased in HCC of TCGA database, and MT genes family were located within a TAD of 1.2 Mb at 16q13 in order, and CTCF binding sites were distributed at the both sites of MT gene clusters. Furthermore, CRISPR/Cas9 was employed to destroy the CTCF binding sites at the vicinity of the MT family in human liver hepatocellular carcinoma (HCC) cell lines Huh-7 and HepG2. And the presence of up-regulated transcription of MTs were observed in Huh-7 and HepG2 cells compared to normal liver CRL-12461 cells. Moreover, the presence of the varying DNA interplay as well as H3K4me3 and H3K9me3 modification on different MT genes were observed after CTCF binding domain destruction compared to the control using chromosome conformation capture (3C) and chromatin immunoprecipitation (ChIP). Our results determined a potential way to regulate the transcription of a series of genes via changing the local genomic organization for diseases treatment.
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Affiliation(s)
- Wenjing Gong
- Department of Oncology, Yantai Yuhuangding Hospital, Yantai, Shandong, 264001, China
| | - Youde Liu
- Department of Hepatology, Yantai Infectious Disease Hospital, Yantai, Shandong, 264001, China
| | - Huajun Qu
- Department of Oncology, Yantai Yuhuangding Hospital, Yantai, Shandong, 264001, China
| | - Aina Liu
- Department of Oncology, Yantai Yuhuangding Hospital, Yantai, Shandong, 264001, China
| | - Ping Sun
- Department of Oncology, Yantai Yuhuangding Hospital, Yantai, Shandong, 264001, China
| | - Xiumei Wang
- Department of Oncology, Yantai Yuhuangding Hospital, Yantai, Shandong, 264001, China.
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24
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Le TBK. Chromosome Conformation Capture with Deep Sequencing to Study the Roles of the Structural Maintenance of Chromosomes Complex In Vivo. Methods Mol Biol 2019; 2004:105-118. [PMID: 31147913 DOI: 10.1007/978-1-4939-9520-2_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent applications of chromosome conformation capture with deep sequencing (Hi-C and other C techniques) has enabled high-throughput investigations and driven major advances in understanding chromosome organization in bacteria and eukaryotes. C techniques reveal systematically the identities of interacting DNA and the frequency of each interaction in vivo. Beyond a bird's-eye view survey of the global chromosome architecture, C techniques together with genetic perturbation have proven to be powerful in understanding factors that shape chromosome architectures. The structural maintenance of chromosomes (SMC) proteins play major roles in organizing the chromosomes from bacteria to humans, and C techniques have contributed to understanding their mechanism and impact on genome organization in a cellular context. Here, I describe a Hi-C protocol, a variant of C techniques, to construct genome-wide DNA contact maps for bacteria. This protocol is optimized for the gram-negative bacterium Caulobacter crescentus, but it can be readily adapted for any bacterial species of interest.
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Affiliation(s)
- Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK.
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25
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Abstract
Chromosome organization, DNA replication, and transcription are only some of the processes relying on dynamic and highly regulated protein-DNA interactions. Here, we describe a biochemical assay to study the molecular details of associations between ring-shaped protein complexes and chromosomes in the context of living cells. Any protein complex embracing chromosomal DNA can be enriched by this method, allowing for the underlying loading mechanisms to be investigated.
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26
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Abstract
Recent imaging, molecular, and computational modeling studies have greatly enhanced our knowledge of how eukaryotic chromosomes are folded in the nuclear space. This work has begun to reveal how 3D genome structure contributes to various DNA-mediated metabolic activities such as replication, transcription, recombination, and repair. Failure of proper DNA repair can lead to the chromosomal translocations observed in human cancers and other diseases. Questions about the role of 3D genome structure in translocation mechanisms have interested scientists for decades. Recent applications of imaging and Chromosome Conformation Capture approaches have clarified the influence of proximal positioning of chromosomal domains and gene loci on the formation of chromosomal translocations. These approaches have revealed the importance of 3D genome structure not only in translocation partner selection, but also in repair efficiency, likelihood of DNA damage, and the biological implications of translocations. This chapter focuses on our current understanding of the role of 3D genome structure in chromosome translocation formation and its potential implications in disease outcome.
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Oluwadare O, Cheng J. ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data. BMC Bioinformatics 2017; 18:480. [PMID: 29137603 PMCID: PMC5686814 DOI: 10.1186/s12859-017-1931-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/06/2017] [Indexed: 11/10/2022] Open
Abstract
Background With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-C technique can generate genome-wide chromosomal interaction (contact) data, which can be used to investigate the higher-level organization of chromosomes, such as Topologically Associated Domains (TAD), i.e., locally packed chromosome regions bounded together by intra chromosomal contacts. The identification of the TADs for a genome is useful for studying gene regulation, genomic interaction, and genome function. Results Here, we formulate the TAD identification problem as an unsupervised machine learning (clustering) problem, and develop a new TAD identification method called ClusterTAD. We introduce a novel method to represent chromosomal contacts as features to be used by the clustering algorithm. Our results show that ClusterTAD can accurately predict the TADs on a simulated Hi-C data. Our method is also largely complementary and consistent with existing methods on the real Hi-C datasets of two mouse cells. The validation with the chromatin immunoprecipitation (ChIP) sequencing (ChIP-Seq) data shows that the domain boundaries identified by ClusterTAD have a high enrichment of CTCF binding sites, promoter-related marks, and enhancer-related histone modifications. Conclusions As ClusterTAD is based on a proven clustering approach, it opens a new avenue to apply a large array of clustering methods developed in the machine learning field to the TAD identification problem. The source code, the results, and the TADs generated for the simulated and real Hi-C datasets are available here: https://github.com/BDM-Lab/ClusterTAD.
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Affiliation(s)
- Oluwatosin Oluwadare
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO, 65211, USA
| | - Jianlin Cheng
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO, 65211, USA. .,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
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Ghan R, Petereit J, Tillett RL, Schlauch KA, Toubiana D, Fait A, Cramer GR. The common transcriptional subnetworks of the grape berry skin in the late stages of ripening. BMC Plant Biol 2017; 17:94. [PMID: 28558655 PMCID: PMC5450095 DOI: 10.1186/s12870-017-1043-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/22/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. RESULTS To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26 °Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock. CONCLUSIONS A common set of differentially expressed genes and gene subnetworks from seven different cultivars were examined in the skin of the late stages of grapevine berry ripening. A densely connected gene subnetwork was elucidated involving a complex interaction of berry senescent processes (autophagy), catabolism, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. Hypotheses were induced from these data sets involving sugar accumulation, light, autophagy, epigenetic regulation, and fruit development. This work provides a better understanding of berry development and the transcriptional processes involved in the late stages of ripening.
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Affiliation(s)
- Ryan Ghan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
| | - Juli Petereit
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - Richard L. Tillett
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - Karen A. Schlauch
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - David Toubiana
- Telekom Innovation, Laboratories and Cyber Security Research Center, Department of Information, Systems Engineering, Ben Gurion University, Beer Sheva, Israel
| | - Aaron Fait
- Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, 84990 Midreshet Ben-Gurion, Israel
| | - Grant R. Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
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Badrinarayanan A, Leake MC. Using Fluorescence Recovery After Photobleaching (FRAP) to Study Dynamics of the Structural Maintenance of Chromosome (SMC) Complex In Vivo. Methods Mol Biol 2016; 1431:37-46. [PMID: 27283300 DOI: 10.1007/978-1-4939-3631-1_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The SMC complex, MukBEF, is important for chromosome organization and segregation in Escherichia coli. Fluorescently tagged MukBEF forms distinct spots (or "foci") in the cell, where it is thought to carry out most of its chromosome associated activities. This chapter outlines the technique of Fluorescence Recovery After Photobleaching (FRAP) as a method to study the properties of YFP-tagged MukB in fluorescent foci. This method can provide important insight into the dynamics of MukB on DNA and be used to study its biochemical properties in vivo.
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Lagomarsino MC, Espéli O, Junier I. From structure to function of bacterial chromosomes: Evolutionary perspectives and ideas for new experiments. FEBS Lett 2015; 589:2996-3004. [PMID: 26171924 DOI: 10.1016/j.febslet.2015.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 12/11/2022]
Abstract
The link between chromosome structure and function is a challenging open question because chromosomes in vivo are highly dynamic and arduous to manipulate. Here, we examine several promising approaches to tackle this question specifically in bacteria, by integrating knowledge from different sources. Toward this end, we first provide a brief overview of experimental tools that have provided insights into the description of the bacterial chromosome, including genetic, biochemical and fluorescence microscopy techniques. We then explore the possibility of using comparative genomics to isolate functionally important features of chromosome organization, exploiting the fact that features shared between phylogenetically distant bacterial species reflect functional significance. Finally, we discuss possible future perspectives from the field of experimental evolution. Specifically, we propose novel experiments in which bacteria could be screened and selected on the basis of the structural properties of their chromosomes.
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Affiliation(s)
| | - Olivier Espéli
- CIRB-Collège de France, CNRS UMR 7241, INSERM U1050, Paris, France
| | - Ivan Junier
- Laboratoire Adaptation et Pathogénie des Micro-organismes - UMR 5163, Université Grenoble 1, CNRS, BP 170, F-38042 Grenoble Cedex 9, France; Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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