1
|
Lawson HA, Liang Y, Wang T. Transposable elements in mammalian chromatin organization. Nat Rev Genet 2023; 24:712-723. [PMID: 37286742 DOI: 10.1038/s41576-023-00609-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2023] [Indexed: 06/09/2023]
Abstract
Transposable elements (TEs) are mobile DNA elements that comprise almost 50% of mammalian genomic sequence. TEs are capable of making additional copies of themselves that integrate into new positions in host genomes. This unique property has had an important impact on mammalian genome evolution and on the regulation of gene expression because TE-derived sequences can function as cis-regulatory elements such as enhancers, promoters and silencers. Now, advances in our ability to identify and characterize TEs have revealed that TE-derived sequences also regulate gene expression by both maintaining and shaping 3D genome architecture. Studies are revealing how TEs contribute raw sequence that can give rise to the structures that shape chromatin organization, and thus gene expression, allowing for species-specific genome innovation and evolutionary novelty.
Collapse
Affiliation(s)
- Heather A Lawson
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Yonghao Liang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO, USA.
| |
Collapse
|
2
|
Consistencies and contradictions in different polymer models of chromatin architecture. Comput Struct Biotechnol J 2023; 21:1084-1091. [PMID: 36789261 PMCID: PMC9900451 DOI: 10.1016/j.csbj.2023.01.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Genetic information is stored in very long DNA molecules, which are folded to form chromatin, a similarly long polymer fibre that is ultimately organised into chromosomes. The organisation of chromatin is fundamental to many cellular functions, from the expression of the genetic information to cell division. As a long polymer, chromatin is very flexible and may adopt a myriad of shapes. Globally, the polymer physics governing chromatin dynamics is very well understood. But chromatin is not uniform and regions of it, with chemical modifications and bound effectors, form domains and compartments through mechanisms not yet clear. Polymer models have been successfully used to investigate these mechanisms to explain cytological observations and build hypothesis for experimental validation. Many different approaches to conceptualise chromatin in polymer models can be envisioned and each reflects different aspects. Here, we compare recent approaches that aim at reproducing prominent features of interphase chromatin organisation: the compartmentalisation into eu- and heterochromatin compartments, the formation of a nucleolus, chromatin loops and the rosette and Rabl conformations of interphase chromosomes. We highlight commonalities and contradictions that point to a modulation of the mechanisms involved to fine degree. Consolidating models will require the inclusion of yet hidden or neglected parameters.
Collapse
|
3
|
Dyer OT, Ball RC. Surfactancy in a tadpole model of proteins. J R Soc Interface 2022; 19:20220172. [PMID: 36195115 PMCID: PMC9532023 DOI: 10.1098/rsif.2022.0172] [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] [Indexed: 11/07/2022] Open
Abstract
We model the environment of eukaryotic nuclei by representing macromolecules by only their entropic properties, with globular molecules represented by spherical colloids and flexible molecules by polymers. We put particular focus on proteins with both globular and intrinsically disordered regions, which we represent with 'tadpole' constructed by grafting single polymers and colloids together. In Monte Carlo simulations, we find these tadpoles support phase separation via depletion flocculation, and demonstrate several surfactant behaviours, including being found preferentially at interfaces and forming micelles in single phase solution. Furthermore, the model parameters can be tuned to give a tadpole a preference for either bulk phase. However, we find entropy too weak to drive these behaviours by itself at likely biological concentrations.
Collapse
Affiliation(s)
- O. T. Dyer
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - R. C. Ball
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| |
Collapse
|
4
|
Nesterov SV, Ilyinsky NS, Uversky VN. Liquid-liquid phase separation as a common organizing principle of intracellular space and biomembranes providing dynamic adaptive responses. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119102. [PMID: 34293345 DOI: 10.1016/j.bbamcr.2021.119102] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 02/07/2023]
Abstract
This work is devoted to the phenomenon of liquid-liquid phase separation (LLPS), which has come to be recognized as fundamental organizing principle of living cells. We distinguish separation processes with different dimensions. Well-known 3D-condensation occurs in aqueous solution and leads to membraneless organelle (MLOs) formation. 2D-films may be formed near membrane surfaces and lateral phase separation (membrane rafts) occurs within the membranes themselves. LLPS may also occur on 1D structures like DNA and the cyto- and nucleoskeleton. Phase separation provides efficient transport and sorting of proteins and metabolites, accelerates the assembly of metabolic and signaling complexes, and mediates stress responses. In this work, we propose a model in which the processes of polymerization (1D structures), phase separation in membranes (2D structures), and LLPS in the volume (3D structures) influence each other. Disordered proteins and whole condensates may provide membrane raft separation or polymerization of specific proteins. On the other hand, 1D and 2D structures with special composition or embedded IDRs can nucleate condensates. We hypothesized that environmental change may trigger a LLPS which can propagate within the cell interior moving along the cytoskeleton or as an autowave. New phase propagation quickly and using a low amount of energy adjusts cell signaling and metabolic systems to new demands. Cumulatively, the interconnected phase separation phenomena in different dimensions represent a previously unexplored system of intracellular communication and regulation which cannot be ignored when considering both physiological and pathological cell processes.
Collapse
Affiliation(s)
- Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia; Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow 123182, Russia.
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA.
| |
Collapse
|
5
|
Vitkunaite A, Laurinaviciene A, Plancoulaine B, Rasmusson A, Levenson R, Shribak M, Laurinavicius A. Intranuclear birefringent inclusions in paraffin sections by polychromatic polarization microscopy. Sci Rep 2021; 11:6275. [PMID: 33737593 PMCID: PMC7973427 DOI: 10.1038/s41598-021-85667-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/03/2021] [Indexed: 11/25/2022] Open
Abstract
Intranuclear birefringent inclusions (IBI) found in various cell types in paraffin-embedded tissue sections have long been considered to be a tissue processing artifact, although an association with biological processes has been suggested. We applied polychromatic polarization microscopy to image their spatial organization. Our study provides evidence that IBI are caused by liquid paraffin-macromolecular crystals formed during paraffin-embedding procedures within cells and potentially reflect an active transcriptional status.
Collapse
Affiliation(s)
- Aiste Vitkunaite
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Aida Laurinaviciene
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania.,Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Benoit Plancoulaine
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,ANTICIPE, Inserm (UMR 1086), Cancer Center F. Baclesse, Normandy University, Caen, France
| | - Allan Rasmusson
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania.,Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Richard Levenson
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,Department of Pathology and Laboratory Medicine, UC Davis Health, Sacramento, CA, USA
| | - Michael Shribak
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,Marine Biological Laboratory of University of Chicago, Woods Hole, MA, USA
| | - Arvydas Laurinavicius
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania. .,Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.
| |
Collapse
|
6
|
Singh PB, Newman AG. On the relations of phase separation and Hi-C maps to epigenetics. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191976. [PMID: 32257349 PMCID: PMC7062049 DOI: 10.1098/rsos.191976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/03/2020] [Indexed: 05/10/2023]
Abstract
The relationship between compartmentalization of the genome and epigenetics is long and hoary. In 1928, Heitz defined heterochromatin as the largest differentiated chromatin compartment in eukaryotic nuclei. Müller's discovery of position-effect variegation in 1930 went on to show that heterochromatin is a cytologically visible state of heritable (epigenetic) gene repression. Current insights into compartmentalization have come from a high-throughput top-down approach where contact frequency (Hi-C) maps revealed the presence of compartmental domains that segregate the genome into heterochromatin and euchromatin. It has been argued that the compartmentalization seen in Hi-C maps is owing to the physiochemical process of phase separation. Oddly, the insights provided by these experimental and conceptual advances have remained largely silent on how Hi-C maps and phase separation relate to epigenetics. Addressing this issue directly in mammals, we have made use of a bottom-up approach starting with the hallmarks of constitutive heterochromatin, heterochromatin protein 1 (HP1) and its binding partner the H3K9me2/3 determinant of the histone code. They are key epigenetic regulators in eukaryotes. Both hallmarks are also found outside mammalian constitutive heterochromatin as constituents of larger (0.1-5 Mb) heterochromatin-like domains and smaller (less than 100 kb) complexes. The well-documented ability of HP1 proteins to function as bridges between H3K9me2/3-marked nucleosomes contributes to polymer-polymer phase separation that packages epigenetically heritable chromatin states during interphase. Contacts mediated by HP1 'bridging' are likely to have been detected in Hi-C maps, as evidenced by the B4 heterochromatic subcompartment that emerges from contacts between large KRAB-ZNF heterochromatin-like domains. Further, mutational analyses have revealed a finer, innate, compartmentalization in Hi-C experiments that probably reflect contacts involving smaller domains/complexes. Proteins that bridge (modified) DNA and histones in nucleosomal fibres-where the HP1-H3K9me2/3 interaction represents the most evolutionarily conserved paradigm-could drive and generate the fundamental compartmentalization of the interphase nucleus. This has implications for the mechanism(s) that maintains cellular identity, be it a terminally differentiated fibroblast or a pluripotent embryonic stem cell.
Collapse
Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, Nur-Sultan Z05K4F4, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Street 2, Novosibirsk 630090, Russian Federation
| | - Andrew G. Newman
- Institute of Cell and Neurobiology, Charité—Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| |
Collapse
|
7
|
Kim JS. Macromolecular Crowding and Nanoscale Confinement on the Structural Regulation of Chromatins/DNAs. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jun Soo Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea
| |
Collapse
|
8
|
Two Drosophila Neuropeptide Y-like Neurons Define a Reward Module for Transforming Appetitive Odor Representations to Motivation. Sci Rep 2018; 8:11658. [PMID: 30076343 PMCID: PMC6076267 DOI: 10.1038/s41598-018-30113-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/24/2018] [Indexed: 01/15/2023] Open
Abstract
Neuropeptides, many of which are conserved among vertebrate and invertebrate animals, are implicated in the regulation of motivational states that selectively facilitate goal-directed behaviors. After a brief presentation of appetitive odors, Drosophila larvae display an impulsive-like feeding activity in readily accessible palatable food. This innate appetitive response may require coordinated signaling activities of dopamine (DA) and neuropeptide F (NPF; a fly homolog of neuropeptide Y). Here we provide anatomical and functional evidence, at single-cell resolution, that two NPF neurons define a reward module in the highest-order brain region for cognitive processing of food-related olfactory representations. First, laser lesioning of these NPF neurons abolished odor induction of appetitive arousal, while their genetic activation mimicked the behavioral effect of appetitive odors. Further, a circuit analysis shows that each of the two NPF neurons relays its signals to a subset of target neurons in the larval hindbrain-like region. Finally, the NPF neurons discriminatively responded to appetitive odor stimuli, and their odor responses were blocked by targeted lesioning of a pair of dopaminergic third-order olfactory neurons that appear to be presynaptic to the NPF neurons. Therefore, the two NPF neurons contribute to appetitive odor induction of impulsive-like feeding by selectively decoding DA-encoded ascending olfactory inputs and relaying NPF-encoded descending motivational outputs for behavioral execution.
Collapse
|