1
|
Maslan A, Altemose N, Marcus J, Mishra R, Brennan LD, Sundararajan K, Karpen G, Straight AF, Streets A. Mapping protein-DNA interactions with DiMeLo-seq. Nat Protoc 2024:10.1038/s41596-024-01032-9. [PMID: 39237830 DOI: 10.1038/s41596-024-01032-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 06/04/2024] [Indexed: 09/07/2024]
Abstract
We recently developed directed methylation with long-read sequencing (DiMeLo-seq) to map protein-DNA interactions genome wide. DiMeLo-seq is capable of mapping multiple interaction sites on single DNA molecules, profiling protein binding in the context of endogenous DNA methylation, identifying haplotype-specific protein-DNA interactions and mapping protein-DNA interactions in repetitive regions of the genome that are difficult to study with short-read methods. With DiMeLo-seq, adenines in the vicinity of a protein of interest are methylated in situ by tethering the Hia5 methyltransferase to an antibody using protein A. Protein-DNA interactions are then detected by direct readout of adenine methylation with long-read, single-molecule DNA sequencing platforms such as Nanopore sequencing. Here we present a detailed protocol and practical guidance for performing DiMeLo-seq. This protocol can be run on nuclei from fresh, lightly fixed or frozen cells. The protocol requires 1-2 d for performing in situ targeted methylation, 1-5 d for library preparation depending on desired fragment length and 1-3 d for Nanopore sequencing depending on desired sequencing depth. The protocol requires basic molecular biology skills and equipment, as well as access to a Nanopore sequencer. We also provide a Python package, dimelo, for analysis of DiMeLo-seq data.
Collapse
Affiliation(s)
- Annie Maslan
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nicolas Altemose
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jeremy Marcus
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Reet Mishra
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Lucy D Brennan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Gary Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of BioEngineering and BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
2
|
Lou J, Deng Q, Zhang X, Bell CC, Das AB, Bediaga NG, Zlatic CO, Johanson TM, Allan RS, Griffin MDW, Paradkar P, Harvey KF, Dawson MA, Hinde E. Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture. Nucleic Acids Res 2024:gkae720. [PMID: 39193905 DOI: 10.1093/nar/gkae720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 07/29/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Our understanding of heterochromatin nanostructure and its capacity to mediate gene silencing in a living cell has been prevented by the diffraction limit of optical microscopy. Thus, here to overcome this technical hurdle, and directly measure the nucleosome arrangement that underpins this dense chromatin state, we coupled fluorescence lifetime imaging microscopy (FLIM) of Förster resonance energy transfer (FRET) between histones core to the nucleosome, with molecular editing of heterochromatin protein 1 alpha (HP1α). Intriguingly, this super-resolved readout of nanoscale chromatin structure, alongside fluorescence fluctuation spectroscopy (FFS) and FLIM-FRET analysis of HP1α protein-protein interaction, revealed nucleosome arrangement to be differentially regulated by HP1α oligomeric state. Specifically, we found HP1α monomers to impart a previously undescribed global nucleosome spacing throughout genome architecture that is mediated by trimethylation on lysine 9 of histone H3 (H3K9me3) and locally reduced upon HP1α dimerisation. Collectively, these results demonstrate HP1α to impart a dual action on chromatin that increases the dynamic range of nucleosome proximity. We anticipate that this finding will have important implications for our understanding of how live cell heterochromatin structure regulates genome function.
Collapse
Affiliation(s)
- Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Qiji Deng
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Xiaomeng Zhang
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Andrew B Das
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Naiara G Bediaga
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Courtney O Zlatic
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - PrasadN Paradkar
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong3220, Australia
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Anatomy and Developmental Biology and Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Elizabeth Hinde
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| |
Collapse
|
3
|
Atinbayeva N, Valent I, Zenk F, Loeser E, Rauer M, Herur S, Quarato P, Pyrowolakis G, Gomez-Auli A, Mittler G, Cecere G, Erhardt S, Tiana G, Zhan Y, Iovino N. Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos. EMBO J 2024; 43:2685-2714. [PMID: 38831123 PMCID: PMC11217351 DOI: 10.1038/s44318-024-00127-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024] Open
Abstract
Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 (H3K9me3) and recruitment of its epigenetic reader, heterochromatin protein 1a (HP1a), are hallmarks of constitutive heterochromatin. Here, we show that H3K9me3 is transmitted from the maternal germline to the next generation. Maternally inherited H3K9me3, and the histone methyltransferases (HMT) depositing it, are required for the organization of constitutive heterochromatin: early embryos lacking H3K9 methylation display de-condensation of pericentromeric regions, centromere-centromere de-clustering, mitotic defects, and nuclear shape irregularities, resulting in embryo lethality. Unexpectedly, quantitative CUT&Tag and 4D microscopy measurements of HP1a coupled with biophysical modeling revealed that H3K9me2/3 is largely dispensable for HP1a recruitment. Instead, the main function of H3K9me2/3 at this developmental stage is to drive HP1a clustering and subsequent heterochromatin compaction. Our results show that HP1a binding to constitutive heterochromatin in the absence of H3K9me2/3 is not sufficient to promote proper embryo development and heterochromatin formation. The loss of H3K9 HMTs and H3K9 methylation alters genome organization and hinders embryonic development.
Collapse
Affiliation(s)
- Nazerke Atinbayeva
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79085, Freiburg im Breisgau, Germany
| | - Iris Valent
- Karlsruhe Institute of Technology (KIT), Zoological Institute, 76131, Karlsruhe, Germany
| | - Fides Zenk
- Brain Mind Institute, School of Life Sciences EPFL, SV3809, 1015, Lausanne, Switzerland
| | - Eva Loeser
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Michael Rauer
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Shwetha Herur
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Piergiuseppe Quarato
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Giorgos Pyrowolakis
- Centre for Biological signaling studies, University of Freiburg, 79104, Freiburg im Breisgau, Germany
| | - Alejandro Gomez-Auli
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Germano Cecere
- Institute Pasteur, Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, UMR3738, CNRS, 75724, Cedex 15, Paris, France
| | - Sylvia Erhardt
- Karlsruhe Institute of Technology (KIT), Zoological Institute, 76131, Karlsruhe, Germany
| | - Guido Tiana
- Università degli Studi di Milano and INFN, Milan, Italy
| | - Yinxiu Zhan
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milan, Italy.
| | - Nicola Iovino
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany.
| |
Collapse
|
4
|
Salari H, Fourel G, Jost D. Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization. Nat Commun 2024; 15:5393. [PMID: 38918438 PMCID: PMC11199603 DOI: 10.1038/s41467-024-49727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Although our understanding of the involvement of heterochromatin architectural factors in shaping nuclear organization is improving, there is still ongoing debate regarding the role of active genes in this process. In this study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate the relationship between gene transcription and 3D gene folding. Our analysis uncovers a nonmonotonic - globally positive - correlation between intragenic contact density and Pol II occupancy, independent of cohesin-based loop extrusion. Through the development of a biophysical model integrating the role of transcription dynamics within a polymer model of chromosome organization, we demonstrate that Pol II-mediated attractive interactions with limited valency between transcribed regions yield quantitative predictions consistent with chromosome-conformation-capture and live-imaging experiments. Our work provides compelling evidence that transcriptional activity shapes the 4D genome through Pol II-mediated micro-compartmentalization.
Collapse
Affiliation(s)
- Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
- École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007, Lyon, France.
| | - Geneviève Fourel
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
| |
Collapse
|
5
|
Reckard AT, Pandeya A, Voris JM, Gonzalez Cruz CG, Oluwadare O, Klocko AD. A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression in Neurospora crassa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597955. [PMID: 39229016 PMCID: PMC11370578 DOI: 10.1101/2024.06.07.597955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Genome organization is essential for proper function, including gene expression. In metazoan genome organization, chromatin loops and Topologically Associated Domains (TADs) facilitate local gene clustering, while chromosomes form distinct nuclear territories characterized by compartmentalization of silent heterochromatin at the nuclear periphery and active euchromatin in the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation, where heterochromatic centromeres and telomeres independently cluster at the nuclear membrane, while interspersed heterochromatic loci in Neurospora aggregate across megabases of linear genomic distance for forming TAD-like structures. However, the role of individual heterochromatic loci in normal genome organization and function is unknown. Here, we examined the genome organization of a Neurospora strain harboring a ~47.4 kilobase facultative (temporarily silent) heterochromatic region deletion, as well as the genome organization of a strain deleted of a 110.6 kilobase permanently silent constitutive heterochromatic region. While the facultative heterochromatin deletion had little effect on local chromatin structure, the constitutive heterochromatin deletion altered local TAD-like structures, gene expression, and the predicted 3D genome structure by qualitatively repositioning genes into the nucleus center. Our work elucidates the role of individual heterochromatic regions for genome organization and function.
Collapse
Affiliation(s)
- Andrew T Reckard
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Abhishek Pandeya
- Department of Computer Science, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Jacob M Voris
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Carlos G Gonzalez Cruz
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Oluwatosin Oluwadare
- Department of Computer Science, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Andrew D Klocko
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| |
Collapse
|
6
|
Stutzman AV, Hill CA, Armstrong RL, Gohil R, Duronio RJ, Dowen JM, McKay DJ. Heterochromatic 3D genome organization is directed by HP1a- and H3K9-dependent and independent mechanisms. Mol Cell 2024; 84:2017-2035.e6. [PMID: 38795706 PMCID: PMC11185254 DOI: 10.1016/j.molcel.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 03/07/2024] [Accepted: 05/02/2024] [Indexed: 05/28/2024]
Abstract
Whether and how histone post-translational modifications and the proteins that bind them drive 3D genome organization remains unanswered. Here, we evaluate the contribution of H3K9-methylated constitutive heterochromatin to 3D genome organization in Drosophila tissues. We find that the predominant organizational feature of wild-type tissues is the segregation of euchromatic chromosome arms from heterochromatic pericentromeres. Reciprocal perturbation of HP1a⋅H3K9me binding, using a point mutation in the HP1a chromodomain or replacement of the replication-dependent histone H3 with H3K9R mutant histones, revealed that HP1a binding to methylated H3K9 in constitutive heterochromatin is required to limit contact frequency between pericentromeres and chromosome arms and regulate the distance between arm and pericentromeric regions. Surprisingly, the self-association of pericentromeric regions is largely preserved despite the loss of H3K9 methylation and HP1a occupancy. Thus, the HP1a⋅H3K9 interaction contributes to but does not solely drive the segregation of euchromatin and heterochromatin inside the nucleus.
Collapse
Affiliation(s)
- Alexis V Stutzman
- Curriculum in Genetics & Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christina A Hill
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robin L Armstrong
- Curriculum in Genetics & Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Riya Gohil
- Curriculum in Genetics & Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Jill M Dowen
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Daniel J McKay
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
| |
Collapse
|
7
|
Magnitov M, de Wit E. Attraction and disruption: how loop extrusion and compartmentalisation shape the nuclear genome. Curr Opin Genet Dev 2024; 86:102194. [PMID: 38636335 PMCID: PMC11190842 DOI: 10.1016/j.gde.2024.102194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 03/21/2024] [Accepted: 03/31/2024] [Indexed: 04/20/2024]
Abstract
Chromatin loops, which bring two distal loci of the same chromosome into close physical proximity, are the ubiquitous units of the three-dimensional genome. Recent advances in understanding the spatial organisation of chromatin suggest that several distinct mechanisms control chromatin interactions, such as loop extrusion by cohesin complexes, compartmentalisation by phase separation, direct protein-protein interactions and others. Here, we review different types of chromatin loops and highlight the factors and processes involved in their regulation. We discuss how loop extrusion and compartmentalisation shape chromatin interactions and how these two processes can either positively or negatively influence each other.
Collapse
Affiliation(s)
- Mikhail Magnitov
- Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. https://twitter.com/@MMagnitov
| | - Elzo de Wit
- Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
| |
Collapse
|
8
|
Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H. Genome folding principles uncovered in condensin-depleted mitotic chromosomes. Nat Genet 2024; 56:1213-1224. [PMID: 38802567 DOI: 10.1038/s41588-024-01759-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 04/18/2024] [Indexed: 05/29/2024]
Abstract
During mitosis, condensin activity is thought to interfere with interphase chromatin structures. To investigate genome folding principles in the absence of chromatin loop extrusion, we codepleted condensin I and condensin II, which triggered mitotic chromosome compartmentalization in ways similar to that in interphase. However, two distinct euchromatic compartments, indistinguishable in interphase, emerged upon condensin loss with different interaction preferences and dependencies on H3K27ac. Constitutive heterochromatin gradually self-aggregated and cocompartmentalized with facultative heterochromatin, contrasting with their separation during interphase. Notably, some cis-regulatory element contacts became apparent even in the absence of CTCF/cohesin-mediated structures. Heterochromatin protein 1 (HP1) proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M to G1 phase in the combined absence of HP1α, HP1β and HP1γ, constitutive heterochromatin compartments are normally re-established. In sum, condensin-deficient mitotic chromosomes illuminate forces of genome compartmentalization not identified in interphase cells.
Collapse
Affiliation(s)
- Han Zhao
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yinzhi Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - En Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Fuhai Liu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Lirong Shu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Dannan Jing
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Baiyue Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Manzhu Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Basic Medicine, Capital Medical University, Beijing, China
| | - Fengnian Shan
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Pharmacology, South China University of Technology, Guangzhou, China
| | - Lin Zhang
- School of Biological Science, Hongkong University, Hongkong, China
| | - Jessica C Lam
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susannah C Midla
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China.
| |
Collapse
|
9
|
Harris HL, Rowley MJ. Mechanistic drivers of chromatin organization into compartments. Curr Opin Genet Dev 2024; 86:102193. [PMID: 38626581 DOI: 10.1016/j.gde.2024.102193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/11/2024] [Accepted: 03/26/2024] [Indexed: 04/18/2024]
Abstract
The human genome is not just a simple string of DNA, it is a complex and dynamic entity intricately folded within the cell's nucleus. This three-dimensional organization of chromatin, the combination of DNA and proteins in the nucleus, is crucial for many biological processes and has been prominently studied for its intricate relationship to gene expression. Indeed, the transcriptional machinery does not operate in isolation but interacts intimately with the folded chromatin structure. Techniques for chromatin conformation capture, including genome-wide sequencing approaches, have revealed key organizational features of chromatin, such as the formation of loops by CCCTC-binding factor (CTCF) and the division of loci into chromatin compartments. While much of the recent research and reviews have focused on CTCF loops, we discuss several new revelations that have emerged concerning chromatin compartments, with a particular focus on what is known about mechanistic drivers of compartmentalization. These insights challenge the traditional views of chromatin organization and reveal the complexity behind the formation and maintenance of chromatin compartments.
Collapse
Affiliation(s)
- Hannah L Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha 68198, NE, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha 68198, NE, USA.
| |
Collapse
|
10
|
Yang J, Chung CI, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X. MYC phase separation selectively modulates the transcriptome. Nat Struct Mol Biol 2024:10.1038/s41594-024-01322-6. [PMID: 38811792 DOI: 10.1038/s41594-024-01322-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/22/2024] [Indexed: 05/31/2024]
Abstract
Dysregulation and enhanced expression of MYC transcription factors (TFs) including MYC and MYCN contribute to the majority of human cancers. For example, MYCN is amplified up to several hundredfold in high-risk neuroblastoma. The resulting overexpression of N-myc aberrantly activates genes that are not activated at low N-myc levels and drives cell proliferation. Whether increasing N-myc levels simply mediates binding to lower-affinity binding sites in the genome or fundamentally changes the activation process remains unclear. One such activation mechanism that could become important above threshold levels of N-myc is the formation of aberrant transcriptional condensates through phase separation. Phase separation has recently been linked to transcriptional regulation, but the extent to which it contributes to gene activation remains an open question. Here we characterized the phase behavior of N-myc and showed that it can form dynamic condensates that have transcriptional hallmarks. We tested the role of phase separation in N-myc-regulated transcription by using a chemogenetic tool that allowed us to compare non-phase-separated and phase-separated conditions at equivalent N-myc levels, both of which showed a strong impact on gene expression compared to no N-myc expression. Interestingly, we discovered that only a small percentage (<3%) of N-myc-regulated genes is further modulated by phase separation but that these events include the activation of key oncogenes and the repression of tumor suppressors. Indeed, phase separation increases cell proliferation, corroborating the biological effects of the transcriptional changes. However, our results also show that >97% of N-myc-regulated genes are not affected by N-myc phase separation, demonstrating that soluble complexes of TFs with the transcriptional machinery are sufficient to activate transcription.
Collapse
Affiliation(s)
- Junjiao Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Chan-I Chung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Koach
- Departments of Neurology, Neurological Surgery, Pediatrics, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Hongjiang Liu
- Institute for Human Genetics, Departments of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ambuja Navalkar
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao He
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Zhimin Ma
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Qian Zhao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoyu Yang
- Institute for Human Genetics, Departments of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Liang He
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yin Shen
- Institute for Human Genetics, Departments of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - William A Weiss
- Departments of Neurology, Neurological Surgery, Pediatrics, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Center, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
11
|
Gurgo J, Walter JC, Fiche JB, Houbron C, Schaeffer M, Cavalli G, Bantignies F, Nollmann M. Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes. Cell Rep 2024; 43:114167. [PMID: 38691452 DOI: 10.1016/j.celrep.2024.114167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 02/15/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024] Open
Abstract
Polycomb (Pc) group proteins are transcriptional regulators with key roles in development, cell identity, and differentiation. Pc-bound chromatin regions form repressive domains that interact in 3D to assemble repressive nuclear compartments. Here, we use multiplexed chromatin imaging to investigate whether Pc compartments involve the clustering of multiple Pc domains during Drosophila development. Notably, 3D proximity between Pc targets is rare and involves predominantly pairwise interactions. These 3D proximities are particularly enhanced in segments where Pc genes are co-repressed. In addition, segment-specific expression of Hox Pc targets leads to their spatial segregation from Pc-repressed genes. Finally, non-Hox Pc targets are more proximal in regions where they are co-expressed. These results indicate that long-range Pc interactions are temporally and spatially regulated during differentiation and development but do not induce frequent clustering of multiple distant Pc genes.
Collapse
Affiliation(s)
- Julian Gurgo
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France
| | - Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France
| | - Christophe Houbron
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France
| | - Marie Schaeffer
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France
| | - Giacomo Cavalli
- Institut de Génétique Humaine, CNRS UMR 9002, Université de Montpellier, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Frédéric Bantignies
- Institut de Génétique Humaine, CNRS UMR 9002, Université de Montpellier, 141 rue de la Cardonille, 34396 Montpellier, France.
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France.
| |
Collapse
|
12
|
Wang H, Yin C, Zhang G, Yang M, Zhu B, Jiang J, Zeng Z. Cold-induced deposition of bivalent H3K4me3-H3K27me3 modification and nucleosome depletion in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:549-564. [PMID: 38184780 DOI: 10.1111/tpj.16624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024]
Abstract
Epigenetic regulation of gene expression plays a crucial role in plant development and environmental adaptation. The H3K4me3 and H3K27me3 have not only been discovered in the regulation of gene expression in multiple biological processes but also in responses to abiotic stresses in plants. However, evidence for the presence of both H3K4me3 and H3K27me3 on the same nucleosome is sporadic. Cold-induced deposition of bivalent H3K4me3-H3K27me3 modifications and nucleosome depletion over a considerable number of active genes is documented in potato tubers and provides clues on an additional role of the bivalent modifications. Limited by the available information of genes encoding PcG/TrxG proteins as well as their corresponding mutants in potatoes, the molecular mechanism underlying the cold-induced deposition of the bivalent mark remains elusive. In this study, we found a similar deposition of the bivalent H3K4me3-H3K27me3 mark over 2129 active genes in cold-treated Arabidopsis Col-0 seedlings. The expression levels of the bivalent mark-associated genes tend to be independent of bivalent modification levels. However, these genes were associated with greater chromatin accessibility, presumably to provide a distinct chromatin environment for gene expression. In mutants clf28 and lhp1, failure to deposit H3K27me3 in active genes upon cold treatment implies that the CLF is potentially involved in cold-induced deposition of H3K27me3, with assistance from LHP1. Failure to deposit H3K4me3 during cold treatment in atx1-2 suggests a regulatory role of ATX1 in the deposition of H3K4me3. In addition, we observed a cold-induced global reduction in nucleosome occupancy, which is potentially mediated by LHP1 in an H3K27me3-dependent manner.
Collapse
Affiliation(s)
- Hao Wang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Chang Yin
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Guoyan Zhang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Miao Yang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Bo Zhu
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University AgBioResearch, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Zixian Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| |
Collapse
|
13
|
Sun J, Qu J, Zhao C, Zhang X, Liu X, Wang J, Wei C, Liu X, Wang M, Zeng P, Tang X, Ling X, Qing L, Jiang S, Chen J, Chen TSR, Kuang Y, Gao J, Zeng X, Huang D, Yuan Y, Fan L, Yu H, Ding J. Precise prediction of phase-separation key residues by machine learning. Nat Commun 2024; 15:2662. [PMID: 38531854 DOI: 10.1038/s41467-024-46901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
Understanding intracellular phase separation is crucial for deciphering transcriptional control, cell fate transitions, and disease mechanisms. However, the key residues, which impact phase separation the most for protein phase separation function have remained elusive. We develop PSPHunter, which can precisely predict these key residues based on machine learning scheme. In vivo and in vitro validations demonstrate that truncating just 6 key residues in GATA3 disrupts phase separation, enhancing tumor cell migration and inhibiting growth. Glycine and its motifs are enriched in spacer and key residues, as revealed by our comprehensive analysis. PSPHunter identifies nearly 80% of disease-associated phase-separating proteins, with frequent mutated pathological residues like glycine and proline often residing in these key residues. PSPHunter thus emerges as a crucial tool to uncover key residues, facilitating insights into phase separation mechanisms governing transcriptional control, cell fate transitions, and disease development.
Collapse
Affiliation(s)
- Jun Sun
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiale Qu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Cai Zhao
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyao Zhang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyu Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jia Wang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyi Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mulan Wang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pengguihang Zeng
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiuxiao Tang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoru Ling
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li Qing
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiahao Chen
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tara S R Chen
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Yalan Kuang
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Jinhang Gao
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Xiaoxi Zeng
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Dongfeng Huang
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Yong Yuan
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
| | - Lili Fan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong, China.
| | - Haopeng Yu
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
| | - Junjun Ding
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China.
| |
Collapse
|
14
|
Chung CI, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X. Phase separation of YAP-MAML2 differentially regulates the transcriptome. Proc Natl Acad Sci U S A 2024; 121:e2310430121. [PMID: 38315854 PMCID: PMC10873646 DOI: 10.1073/pnas.2310430121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/13/2023] [Indexed: 02/07/2024] Open
Abstract
Phase separation (PS) drives the formation of biomolecular condensates that are emerging biological structures involved in diverse cellular processes. Recent studies have unveiled PS-induced formation of several transcriptional factor (TF) condensates that are transcriptionally active, but how strongly PS promotes gene activation remains unclear. Here, we show that the oncogenic TF fusion Yes-associated protein 1-Mastermind like transcriptional coactivator 2 (YAP-MAML2) undergoes PS and forms liquid-like condensates that bear the hallmarks of transcriptional activity. Furthermore, we examined the contribution of PS to YAP-MAML2-mediated gene expression by developing a chemogenetic tool that dissolves TF condensates, allowing us to compare phase-separated and non-phase-separated conditions at identical YAP-MAML2 protein levels. We found that a small fraction of YAP-MAML2-regulated genes is further affected by PS, which include the canonical YAP target genes CTGF and CYR61, and other oncogenes. On the other hand, majority of YAP-MAML2-regulated genes are not affected by PS, highlighting that transcription can be activated effectively by diffuse complexes of TFs with the transcriptional machinery. Our work opens new directions in understanding the role of PS in selective modulation of gene expression, suggesting differential roles of PS in biological processes.
Collapse
Affiliation(s)
- Chan-I. Chung
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
| | - Junjiao Yang
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
| | - Xiaoyu Yang
- Department of Neurology, Institute for Human Genetics, Weill Institute for Neurosciences, University of California, San Francisco, CA94158
| | - Hongjiang Liu
- Department of Neurology, Institute for Human Genetics, Weill Institute for Neurosciences, University of California, San Francisco, CA94158
| | - Zhimin Ma
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Seattle Tumor Translational Research Center, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Yin Shen
- Department of Neurology, Institute for Human Genetics, Weill Institute for Neurosciences, University of California, San Francisco, CA94158
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
| |
Collapse
|
15
|
Ukmar-Godec T, Cima-Omori MS, Yerkesh Z, Eswara K, Yu T, Ramesh R, Riviere G, Ibanez de Opakua A, Fischle W, Zweckstetter M. Multimodal interactions drive chromatin phase separation and compaction. Proc Natl Acad Sci U S A 2023; 120:e2308858120. [PMID: 38048471 PMCID: PMC10723116 DOI: 10.1073/pnas.2308858120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/01/2023] [Indexed: 12/06/2023] Open
Abstract
Gene silencing is intimately connected to DNA condensation and the formation of transcriptionally inactive heterochromatin by Heterochromatin Protein 1α (HP1α). Because heterochromatin foci are dynamic and HP1α can promote liquid-liquid phase separation, HP1α-mediated phase separation has been proposed as a mechanism of chromatin compaction. The molecular basis of HP1α-driven phase separation and chromatin compaction and the associated regulation by trimethylation of lysine 9 in histone 3 (H3K9me3), which is the hallmark of constitutive heterochromatin, is however largely unknown. Using a combination of chromatin compaction and phase separation assays, site-directed mutagenesis, and NMR-based interaction analysis, we show that human HP1α can compact chromatin in the absence of liquid-liquid phase separation. We further demonstrate that H3K9-trimethylation promotes compaction of chromatin arrays through multimodal interactions. The results provide molecular insights into HP1α-mediated chromatin compaction and thus into the role of human HP1α in the regulation of gene silencing.
Collapse
Affiliation(s)
- Tina Ukmar-Godec
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Maria-Sol Cima-Omori
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Zhadyra Yerkesh
- Bioscience Program, Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal23955, Saudi Arabia
| | - Karthik Eswara
- Bioscience Program, Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal23955, Saudi Arabia
| | - Taekyung Yu
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Reshma Ramesh
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Gwladys Riviere
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Alain Ibanez de Opakua
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Wolfgang Fischle
- Bioscience Program, Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal23955, Saudi Arabia
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
| |
Collapse
|
16
|
Scadden AW, Graybill AS, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD. Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa. Proc Natl Acad Sci U S A 2023; 120:e2311249120. [PMID: 37963248 PMCID: PMC10666030 DOI: 10.1073/pnas.2311249120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023] Open
Abstract
Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungus Neurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain-like structures formed by heterochromatic region aggregation. However, insufficient data exist on how histone posttranslational modifications (PTMs), including acetylation, affect genome organization. In Neurospora, the HCHC complex [composed of the proteins HDA-1, CDP-2 (Chromodomain Protein-2), Heterochromatin Protein-1, and CHAP (CDP-2 and HDA-1 Associated Protein)] deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation, and alters the methylation of cytosines in DNA. Here, we assess whether the HCHC complex affects genome organization by performing Hi-C in strains deleted of the cdp-2 or chap genes. CDP-2 loss increases intra- and interchromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone PTMs genome-wide, as CDP-2 deletion increases heterochromatic H4K16 acetylation, yet smaller heterochromatic regions lose H3K9 trimethylation and gain interheterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.
Collapse
Affiliation(s)
- Ashley W. Scadden
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Alayne S. Graybill
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Clayton Hull-Crew
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Tiffany J. Lundberg
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Nickolas M. Lande
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Andrew D. Klocko
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| |
Collapse
|
17
|
Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H. Genome folding principles revealed in condensin-depleted mitotic chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566494. [PMID: 38014261 PMCID: PMC10680603 DOI: 10.1101/2023.11.09.566494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
During mitosis, condensin activity interferes with interphase chromatin structures. Here, we generated condensin-free mitotic chromosomes to investigate genome folding principles. Co-depletion of condensin I and II, but neither alone, triggered mitotic chromosome compartmentalization in ways that differ from interphase. Two distinct euchromatic compartments, indistinguishable in interphase, rapidly emerged upon condensin loss with different interaction preferences and dependence on H3K27ac. Constitutive heterochromatin gradually self-aggregated and co-compartmentalized with the facultative heterochromatin, contrasting with their separation during interphase. While topologically associating domains (TADs) and CTCF/cohesin mediated structural loops remained undetectable, cis-regulatory element contacts became apparent, providing an explanation for their quick re-establishment during mitotic exit. HP1 proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M- to G1-phase in the combined absence of HP1α, HP1β and HP1γ, re-established constitutive heterochromatin compartments normally. In sum, "clean-slate" condensing-deficient mitotic chromosomes illuminate mechanisms of genome compartmentalization not revealed in interphase cells.
Collapse
Affiliation(s)
- Han Zhao
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Yinzhi Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - En Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Fuhai Liu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Lirong Shu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Dannan Jing
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Baiyue Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Manzhu Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- School of Basic medicine, Capital Medical University, Beijing, China
| | - Fengnian Shan
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- School of Pharmacology, South China University of Technology, Guangzhou, Guangdong, China
| | - Lin Zhang
- School of Biological Science, Hongkong University, Hongkong, China
| | - Jessica C. Lam
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susannah C. Midla
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Belinda M. Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Gerd A. Blobel
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| |
Collapse
|
18
|
Depierre D, Perrois C, Schickele N, Lhoumaud P, Abdi-Galab M, Fosseprez O, Heurteau A, Margueron R, Cuvier O. Chromatin in 3D distinguishes dMes-4/NSD and Hypb/dSet2 in protecting genes from H3K27me3 silencing. Life Sci Alliance 2023; 6:e202302038. [PMID: 37684044 PMCID: PMC10491495 DOI: 10.26508/lsa.202302038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Cell type-specific barcoding of genomes requires the establishment of hundreds of heterochromatin domains where heterochromatin-associated repressive complexes hinder chromatin accessibility thereby silencing genes. At heterochromatin-euchromatin borders, regulation of accessibility not only depends on the delimitation of heterochromatin but may also involve interplays with nearby genes and their transcriptional activity, or alternatively on histone modifiers, chromatin barrier insulators, and more global demarcation of chromosomes into 3D compartmentalized domains and topological-associating domain (TADs). Here, we show that depletion of H3K36 di- or tri-methyl histone methyltransferases dMes-4/NSD or Hypb/dSet2 induces reproducible increasing levels of H3K27me3 at heterochromatin borders including in nearby promoters, thereby repressing hundreds of genes. Furthermore, dMes-4/NSD influences genes demarcated by insulators and TAD borders, within chromatin hubs, unlike transcription-coupled action of Hypb/dSet2 that protects genes independently of TADs. Insulator mutants recapitulate the increase of H3K27me3 upon dMes-4/NSD depletion unlike Hypb/dSet2. Hi-C data demonstrate how dMes-4/NSD blocks propagation of long-range interactions onto active regions. Our data highlight distinct mechanisms protecting genes from H3K27me3 silencing, highlighting a direct influence of H3K36me on repressive TADs.
Collapse
Affiliation(s)
- David Depierre
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Charlène Perrois
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Naomi Schickele
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Priscillia Lhoumaud
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Mahdia Abdi-Galab
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Olivier Fosseprez
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Alexandre Heurteau
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Raphaël Margueron
- Institut Curie, Paris Sciences et Lettres Research University; INSERM U934/ CNRS UMR3215, Paris, France
| | - Olivier Cuvier
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| |
Collapse
|
19
|
Pang LY, DeLuca S, Zhu H, Urban JM, Spradling AC. Chromatin and gene expression changes during female Drosophila germline stem cell development illuminate the biology of highly potent stem cells. eLife 2023; 12:RP90509. [PMID: 37831064 PMCID: PMC10575629 DOI: 10.7554/elife.90509] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Highly potent animal stem cells either self renew or launch complex differentiation programs, using mechanisms that are only partly understood. Drosophila female germline stem cells (GSCs) perpetuate without change over evolutionary time and generate cystoblast daughters that develop into nurse cells and oocytes. Cystoblasts initiate differentiation by generating a transient syncytial state, the germline cyst, and by increasing pericentromeric H3K9me3 modification, actions likely to suppress transposable element activity. Relatively open GSC chromatin is further restricted by Polycomb repression of testis or somatic cell-expressed genes briefly active in early female germ cells. Subsequently, Neijre/CBP and Myc help upregulate growth and reprogram GSC metabolism by altering mitochondrial transmembrane transport, gluconeogenesis, and other processes. In all these respects GSC differentiation resembles development of the totipotent zygote. We propose that the totipotent stem cell state was shaped by the need to resist transposon activity over evolutionary timescales.
Collapse
Affiliation(s)
- Liang-Yu Pang
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Steven DeLuca
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Haolong Zhu
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - John M Urban
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Allan C Spradling
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| |
Collapse
|
20
|
Mielczarek O, Rogers CH, Zhan Y, Matheson LS, Stubbington MJT, Schoenfelder S, Bolland DJ, Javierre BM, Wingett SW, Várnai C, Segonds-Pichon A, Conn SJ, Krueger F, Andrews S, Fraser P, Giorgetti L, Corcoran AE. Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes. Cell Rep 2023; 42:113074. [PMID: 37676766 PMCID: PMC10548092 DOI: 10.1016/j.celrep.2023.113074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/28/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
To produce a diverse antibody repertoire, immunoglobulin heavy-chain (Igh) loci undergo large-scale alterations in structure to facilitate juxtaposition and recombination of spatially separated variable (VH), diversity (DH), and joining (JH) genes. These chromosomal alterations are poorly understood. Uncovering their patterns shows how chromosome dynamics underpins antibody diversity. Using tiled Capture Hi-C, we produce a comprehensive map of chromatin interactions throughout the 2.8-Mb Igh locus in progenitor B cells. We find that the Igh locus folds into semi-rigid subdomains and undergoes flexible looping of the VH genes to its 3' end, reconciling two views of locus organization. Deconvolution of single Igh locus conformations using polymer simulations identifies thousands of different structures. This heterogeneity may underpin the diversity of V(D)J recombination events. All three immunoglobulin loci also participate in a highly specific, developmentally regulated network of interchromosomal interactions with genes encoding B cell-lineage factors. This suggests a model of interchromosomal coordination of B cell development.
Collapse
Affiliation(s)
- Olga Mielczarek
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Carolyn H Rogers
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Louise S Matheson
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael J T Stubbington
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Daniel J Bolland
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Biola M Javierre
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Steven W Wingett
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Anne Segonds-Pichon
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Simon J Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Anne E Corcoran
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
| |
Collapse
|
21
|
Scadden AW, Graybill AS, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD. Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547530. [PMID: 37461718 PMCID: PMC10349943 DOI: 10.1101/2023.07.03.547530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungus Neurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures formed by heterochromatic region aggregation. However, insufficient data exists on how histone post-translational modifications, including acetylation, affect genome organization. In Neurospora, the HCHC complex (comprised of the proteins HDA-1, CDP-2, HP1, and CHAP) deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation and alters the methylation of cytosines in DNA. Here, we assess if the HCHC complex affects genome organization by performing Hi-C in strains deleted of the cdp-2 or chap genes. CDP-2 loss increases intra- and inter-chromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone post-translational modifications genome-wide: without CDP-2, heterochromatic H4K16 acetylation is increased, yet smaller heterochromatic regions lose H3K9 trimethylation and gain inter-heterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder, as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.
Collapse
Affiliation(s)
- Ashley W. Scadden
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Alayne S. Graybill
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Clayton Hull-Crew
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Tiffany J. Lundberg
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Nickolas M. Lande
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Andrew D. Klocko
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| |
Collapse
|
22
|
Abstract
Many cellular processes require large-scale rearrangements of chromatin structure. Structural maintenance of chromosomes (SMC) protein complexes are molecular machines that can provide structure to chromatin. These complexes can connect DNA elements in cis, walk along DNA, build and processively enlarge DNA loops and connect DNA molecules in trans to hold together the sister chromatids. These DNA-shaping abilities place SMC complexes at the heart of many DNA-based processes, including chromosome segregation in mitosis, transcription control and DNA replication, repair and recombination. In this Review, we discuss the latest insights into how SMC complexes such as cohesin, condensin and the SMC5-SMC6 complex shape DNA to direct these fundamental chromosomal processes. We also consider how SMC complexes, by building chromatin loops, can counteract the natural tendency of alike chromatin regions to cluster. SMC complexes thus control nuclear organization by participating in a molecular tug of war that determines the architecture of our genome.
Collapse
Affiliation(s)
- Claire Hoencamp
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| |
Collapse
|
23
|
Chen Y, Xie D, Ma X, Xue X, Liu M, Xiao X, Lai C, Xu X, Chen X, Chen Y, Zhang Z, XuHan X, Lai Z, Lin Y. Genome-wide high-throughput chromosome conformation capture analysis reveals hierarchical chromatin interactions during early somatic embryogenesis. PLANT PHYSIOLOGY 2023; 193:555-577. [PMID: 37313777 DOI: 10.1093/plphys/kiad348] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/04/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023]
Abstract
Somatic embryogenesis (SE), like zygotic embryo development, is a progressive process. Early SE is the beginning of a switch from a somatic to an embryogenic state and is an important stage for initiating chromatin reprogramming of SE. Previous studies suggest that changes in chromatin accessibility occur during early SE, although information on the 3D structure of chromatin is not yet available. Here, we present a chromosome-level genome assembly of longan (Dimocarpus longan) using PacBio combined with high-through chromosome conformation capture scaffolding, which resulted in a 446 Mb genome assembly anchored onto 15 scaffolds. During early SE, chromatin was concentrated and then decondensed, and a large number of long terminal repeat retrotransposons (LTR-RTs) were enriched in the local chromatin interaction region, suggesting LTR-RTs were involved in chromatin reorganization. Early SE was accompanied by the transformation from A to B compartments, and the interactions between B compartments were enhanced. Results from chromatin accessibility, monomethylation of histone H3 at lysine 4 (H3K4me1) modification, and transcription analyses further revealed a gene regulatory network for cell wall thickening during SE. Particularly, we found that the H3K4me1 differential peak binding motif showed abnormal activation of ethylene response factor transcription factors and participation in SE. The chromosome-level genomic and multiomics analyses revealed the 3D conformation of chromatin during early SE, providing insight into the molecular mechanisms underlying cell wall thickening and the potential regulatory networks of TFs during early SE in D. longan. These results provide additional clues for revealing the molecular mechanisms of plant SE.
Collapse
Affiliation(s)
- Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Dejian Xie
- Beijing Research Center, Wuhan Frasergen Bioinformatics Co., Ltd, Beijing 100081, China
| | - Xiangwei Ma
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaodong Xue
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Mengyu Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xuechen Xiao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chunwang Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xu XuHan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, Toulouse 31300, France
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| |
Collapse
|
24
|
Mohana G, Dorier J, Li X, Mouginot M, Smith RC, Malek H, Leleu M, Rodriguez D, Khadka J, Rosa P, Cousin P, Iseli C, Restrepo S, Guex N, McCabe BD, Jankowski A, Levine MS, Gambetta MC. Chromosome-level organization of the regulatory genome in the Drosophila nervous system. Cell 2023; 186:3826-3844.e26. [PMID: 37536338 PMCID: PMC10529364 DOI: 10.1016/j.cell.2023.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 03/31/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
Previous studies have identified topologically associating domains (TADs) as basic units of genome organization. We present evidence of a previously unreported level of genome folding, where distant TAD pairs, megabases apart, interact to form meta-domains. Within meta-domains, gene promoters and structural intergenic elements present in distant TADs are specifically paired. The associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. These long-range associations occur in a large fraction of neurons but support transcription in only a subset of neurons. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that two such factors, GAF and CTCF, play direct roles in this process. The relative simplicity of higher-order meta-domain interactions in Drosophila, compared with those previously described in mammals, allowed the demonstration that genomes can fold into highly specialized cell-type-specific scaffolds that enable megabase-scale regulatory associations.
Collapse
Affiliation(s)
- Giriram Mohana
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Julien Dorier
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Xiao Li
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Marion Mouginot
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Rebecca C Smith
- Brain Mind Institute, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Héléna Malek
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marion Leleu
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Rodriguez
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jenisha Khadka
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Patrycja Rosa
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
| | - Pascal Cousin
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Simon Restrepo
- Arcoris bio AG, Lüssirainstrasse 52, 6300 Zug, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Brian D McCabe
- Brain Mind Institute, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Aleksander Jankowski
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland.
| | - Michael S Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | | |
Collapse
|
25
|
Tortora MMC, Brennan LD, Karpen G, Jost D. HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation. Proc Natl Acad Sci U S A 2023; 120:e2211855120. [PMID: 37549295 PMCID: PMC10438847 DOI: 10.1073/pnas.2211855120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 06/28/2023] [Indexed: 08/09/2023] Open
Abstract
The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid-liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Here, using a minimal theoretical framework, we systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3 loci facilitates coacervation in nucleo and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1-chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical cross talk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensate formation in live Drosophila embryos and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics.
Collapse
Affiliation(s)
- Maxime M. C. Tortora
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 69007Lyon, France
| | - Lucy D. Brennan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Gary Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of BioEngineering and BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 69007Lyon, France
| |
Collapse
|
26
|
Theis A, Harrison MM. Reprogramming of three-dimensional chromatin organization in the early embryo. Curr Opin Struct Biol 2023; 81:102613. [PMID: 37224641 PMCID: PMC10524315 DOI: 10.1016/j.sbi.2023.102613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/26/2023]
Abstract
Chromatin organization within the three-dimensional (3D) nuclear space is important for proper gene expression and developmental programming. This organization is established during the dramatic reprogramming that occurs in early embryonic development. Thus, the early embryo is an ideal model for examining the formation and dynamics of 3D chromatin structure. Advances in high-resolution microscopy and single-nucleus genomic analyses have provided fundamental insights into the mechanisms driving genome organization in the early embryo. Here, we highlight recent findings describing the dynamics and driving mechanisms for establishing 3D chromatin organization and discuss the role such organization has on gene regulation in early embryonic development.
Collapse
Affiliation(s)
- Alexandra Theis
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
27
|
Chen Y, Wang L, Guo F, Dai X, Zhang X. Epigenetic reprogramming during the maternal-to-zygotic transition. MedComm (Beijing) 2023; 4:e331. [PMID: 37547174 PMCID: PMC10397483 DOI: 10.1002/mco2.331] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 08/08/2023] Open
Abstract
After fertilization, sperm and oocyte fused and gave rise to a zygote which is the beginning of a new life. Then the embryonic development is monitored and regulated precisely from the transition of oocyte to the embryo at the early stage of embryogenesis, and this process is termed maternal-to-zygotic transition (MZT). MZT involves two major events that are maternal components degradation and zygotic genome activation. The epigenetic reprogramming plays crucial roles in regulating the process of MZT and supervising the normal development of early development of embryos. In recent years, benefited from the rapid development of low-input epigenome profiling technologies, new epigenetic modifications are found to be reprogrammed dramatically and may play different roles during MZT whose dysregulation will cause an abnormal development of embryos even abortion at various stages. In this review, we summarized and discussed the important novel findings on epigenetic reprogramming and the underlying molecular mechanisms regulating MZT in mammalian embryos. Our work provided comprehensive and detailed references for the in deep understanding of epigenetic regulatory network in this key biological process and also shed light on the critical roles for epigenetic reprogramming on embryonic failure during artificial reproductive technology and nature fertilization.
Collapse
Affiliation(s)
- Yurong Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Luyao Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Fucheng Guo
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Xiangpeng Dai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Xiaoling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| |
Collapse
|
28
|
Sun L, Cao Y, Li Z, Liu Y, Yin X, Deng XW, He H, Qian W. Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1966-1982. [PMID: 37154484 DOI: 10.1111/jipb.13502] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023]
Abstract
Higher-order chromatin organization is essential for transcriptional regulation, genome stability maintenance, and other genome functions. Increasing evidence has revealed significant differences in 3D chromatin organization between plants and animals. However, the extent, pattern, and rules of chromatin organization in plants are still unclear. In this study, we systematically identified and characterized long-range chromatin loops in the Arabidopsis 3D genome. We identified hundreds of long-range cis chromatin loops and found their anchor regions are closely associated with H3K27me3 epigenetic modifications. Furthermore, we demonstrated that these chromatin loops are dependent on Polycomb group (PcG) proteins, suggesting that the Polycomb repressive complex 2 (PRC2) complex is essential for establishing and maintaining these novel loops. Although most of these PcG-medicated chromatin loops are stable, many of these loops are tissue-specific or dynamically regulated by different treatments. Interestingly, tandemly arrayed gene clusters and metabolic gene clusters are enriched in anchor regions. Long-range H3K27me3-marked chromatin interactions are associated with the coregulation of specific gene clusters. Finally, we also identified H3K27me3-associated chromatin loops associated with gene clusters in Oryza sativa and Glycine max, indicating that these long-range chromatin loops are conserved in plants. Our results provide novel insights into genome evolution and transcriptional coregulation in plants.
Collapse
Affiliation(s)
- Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Yuxin Cao
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Yi Liu
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xiaochang Yin
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
29
|
Fukuda K, Shimi T, Shimura C, Ono T, Suzuki T, Onoue K, Okayama S, Miura H, Hiratani I, Ikeda K, Okada Y, Dohmae N, Yonemura S, Inoue A, Kimura H, Shinkai Y. Epigenetic plasticity safeguards heterochromatin configuration in mammals. Nucleic Acids Res 2023; 51:6190-6207. [PMID: 37178005 PMCID: PMC10325917 DOI: 10.1093/nar/gkad387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Heterochromatin is a key architectural feature of eukaryotic chromosomes critical for cell type-specific gene expression and genome stability. In the mammalian nucleus, heterochromatin segregates from transcriptionally active genomic regions and exists in large, condensed, and inactive nuclear compartments. However, the mechanisms underlying the spatial organization of heterochromatin need to be better understood. Histone H3 lysine 9 trimethylation (H3K9me3) and lysine 27 trimethylation (H3K27me3) are two major epigenetic modifications that enrich constitutive and facultative heterochromatin, respectively. Mammals have at least five H3K9 methyltransferases (SUV39H1, SUV39H2, SETDB1, G9a and GLP) and two H3K27 methyltransferases (EZH1 and EZH2). In this study, we addressed the role of H3K9 and H3K27 methylation in heterochromatin organization using a combination of mutant cells for five H3K9 methyltransferases and an EZH1/2 dual inhibitor, DS3201. We showed that H3K27me3, which is normally segregated from H3K9me3, was redistributed to regions targeted by H3K9me3 after the loss of H3K9 methylation and that the loss of both H3K9 and H3K27 methylation resulted in impaired condensation and spatial organization of heterochromatin. Our data demonstrate that the H3K27me3 pathway safeguards heterochromatin organization after the loss of H3K9 methylation in mammalian cells.
Collapse
Affiliation(s)
- Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako351-0198, Japan
- School of Biosciences, The University of Melbourne, Royal Parade, 3010 Parkville, Australia
| | - Takeshi Shimi
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Chikako Shimura
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako351-0198, Japan
| | - Takao Ono
- Chromosome Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako 351-0198, Japan
| | - Kenta Onoue
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Satoko Okayama
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Kazuho Ikeda
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| | - Yasushi Okada
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
- Universal Biology Institute (UBI) and International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo113-0033, Japan
- Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka565-0874, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako 351-0198, Japan
| | - Shigenobu Yonemura
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
- Department of Cell Biology, Tokushima University Graduate School of Medicine, Tokushima770-8503, Japan
| | - Azusa Inoue
- Laboratory for Epigenome Inheritance, RIKEN Center for Integrative Medical Sciences, Yokohama230-0045, Japan
- Tokyo Metropolitan University, Hachioji192-0397, Japan
| | - Hiroshi Kimura
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama226-8501, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako351-0198, Japan
| |
Collapse
|
30
|
Marchi E, Zhan Y, Tiana G. Locality of contacts determines the subdiffusion exponents in polymeric models of chromatin. Phys Rev E 2023; 107:064406. [PMID: 37464651 DOI: 10.1103/physreve.107.064406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/06/2023] [Indexed: 07/20/2023]
Abstract
Loop extrusion by motor proteins mediates the attractive interactions in chromatin on the length scale of megabases, providing the polymer with a well-defined structure and at the same time determining its dynamics. The mean-square displacement of chromatin loci varies from a Rouse-like scaling to a more constrained subdiffusion, depending on cell type, genomic region, and time scale. With a simple polymeric model, we show that such a Rouse-like dynamics occurs when the parameters of the model are chosen so that contacts are local along the chain, while in the presence of nonlocal contacts we observe subdiffusion at short time scales with exponents smaller than 0.5. Such exponents are independent of the detailed choice of the parameters and build a master curve that depends only on the mean locality of the resulting contacts. We compare the loop-extrusion model with a polymeric model with static links, showing that also in this case only the presence of nonlocal contacts can produce low-exponent subdiffusion. We interpret these results in terms of a simple analytical model.
Collapse
Affiliation(s)
- Edoardo Marchi
- Department of Physics, Universitá degli Studi di Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Yinxiu Zhan
- Department of Experimental Oncology, European Institute of Oncology IRCCS, via Adamello 16, 20139 Milano, Italy
| | - Guido Tiana
- Department of Physics and Center for Complexity and Biosystems, Universitá degli Studi di Milano and INFN, via Celoria 16, 20133 Milano, Italy
| |
Collapse
|
31
|
Grewal SIS. The molecular basis of heterochromatin assembly and epigenetic inheritance. Mol Cell 2023; 83:1767-1785. [PMID: 37207657 PMCID: PMC10309086 DOI: 10.1016/j.molcel.2023.04.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023]
Abstract
Heterochromatin plays a fundamental role in gene regulation, genome integrity, and silencing of repetitive DNA elements. Histone modifications are essential for the establishment of heterochromatin domains, which is initiated by the recruitment of histone-modifying enzymes to nucleation sites. This leads to the deposition of histone H3 lysine-9 methylation (H3K9me), which provides the foundation for building high-concentration territories of heterochromatin proteins and the spread of heterochromatin across extended domains. Moreover, heterochromatin can be epigenetically inherited during cell division in a self-templating manner. This involves a "read-write" mechanism where pre-existing modified histones, such as tri-methylated H3K9 (H3K9me3), support chromatin association of the histone methyltransferase to promote further deposition of H3K9me. Recent studies suggest that a critical density of H3K9me3 and its associated factors is necessary for the propagation of heterochromatin domains across multiple generations. In this review, I discuss the key experiments that have highlighted the importance of modified histones for epigenetic inheritance.
Collapse
Affiliation(s)
- Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
32
|
Bajpai G, Safran S. Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics. PLoS Comput Biol 2023; 19:e1011142. [PMID: 37228178 DOI: 10.1371/journal.pcbi.1011142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Chromosomes are arranged in distinct territories within the nucleus of animal cells. Recent experiments have shown that these territories overlap at their edges, suggesting partial mixing during interphase. Experiments that knock-down of condensin II proteins during interphase indicate increased chromosome mixing, which demonstrates control of the mixing. In this study, we use a generic polymer simulation to quantify the dynamics of chromosome mixing over time. We introduce the chromosome mixing index, which quantifies the mixing of distinct chromosomes in the nucleus. We find that the chromosome mixing index in a small confinement volume (as a model of the nucleus), increases as a power-law of the time, with the scaling exponent varying non-monotonically with self-interaction and volume fraction. By comparing the chromosome mixing index with both monomer subdiffusion due to (non-topological) intermingling of chromosomes as well as even slower reptation, we show that for relatively large volume fractions, the scaling exponent of the chromosome mixing index is related to Rouse dynamics for relatively weak chromosome attractions and to reptation for strong attractions. In addition, we extend our model to more realistically account for the situation of the Drosophila chromosome by including the heterogeneity of the polymers and their lengths to account for microphase separation of euchromatin and heterochromatin and their interactions with the nuclear lamina. We find that the interaction with the lamina further impedes chromosome mixing.
Collapse
Affiliation(s)
- Gaurav Bajpai
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
33
|
Rang FJ, Kind J, Guerreiro I. The role of heterochromatin in 3D genome organization during preimplantation development. Cell Rep 2023; 42:112248. [PMID: 37059092 DOI: 10.1016/j.celrep.2023.112248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/21/2022] [Accepted: 02/27/2023] [Indexed: 04/16/2023] Open
Abstract
During the early stages of mammalian development, the epigenetic state of the parental genome is completely reprogrammed to give rise to the totipotent embryo. An important aspect of this remodeling concerns the heterochromatin and the spatial organization of the genome. While heterochromatin and genome organization are intricately linked in pluripotent and somatic systems, little is known about their relationship in the totipotent embryo. In this review, we summarize the current knowledge on the reprogramming of both regulatory layers. In addition, we discuss available evidence on their relationship and put this in the context of findings in other systems.
Collapse
Affiliation(s)
- Franka J Rang
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Jop Kind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, the Netherlands; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Houtlaan 4, 6525 XZ Nijmegen, the Netherlands.
| | - Isabel Guerreiro
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, the Netherlands.
| |
Collapse
|
34
|
Ciabrelli F, Rabbani L, Cardamone F, Zenk F, Löser E, Schächtle MA, Mazina M, Loubiere V, Iovino N. CBP and Gcn5 drive zygotic genome activation independently of their catalytic activity. SCIENCE ADVANCES 2023; 9:eadf2687. [PMID: 37083536 PMCID: PMC10121174 DOI: 10.1126/sciadv.adf2687] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Zygotic genome activation (ZGA) is a crucial step of embryonic development. So far, little is known about the role of chromatin factors during this process. Here, we used an in vivo RNA interference reverse genetic screen to identify chromatin factors necessary for embryonic development in Drosophila melanogaster. Our screen reveals that histone acetyltransferases (HATs) and histone deacetylases are crucial ZGA regulators. We demonstrate that Nejire (CBP/EP300 ortholog) is essential for the acetylation of histone H3 lysine-18 and lysine-27, whereas Gcn5 (GCN5/PCAF ortholog) for lysine-9 of H3 at ZGA, with these marks being enriched at all actively transcribed genes. Nonetheless, these HATs activate distinct sets of genes. Unexpectedly, individual catalytic dead mutants of either Nejire or Gcn5 can activate zygotic transcription (ZGA) and transactivate a reporter gene in vitro. Together, our data identify Nejire and Gcn5 as key regulators of ZGA.
Collapse
Affiliation(s)
- Filippo Ciabrelli
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Leily Rabbani
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Francesco Cardamone
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- University of Freiburg, Faculty of Biology, Freiburg im Breisgau, Germany
| | - Fides Zenk
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Eva Löser
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Melanie A. Schächtle
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Marina Mazina
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | | | - Nicola Iovino
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| |
Collapse
|
35
|
Erdel F. Phase transitions in heterochromatin organization. Curr Opin Struct Biol 2023; 80:102597. [PMID: 37087823 DOI: 10.1016/j.sbi.2023.102597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
Heterochromatin formation has been proposed to involve phase transitions on the level of the three-dimensional folding of heterochromatin regions and the liquid-liquid demixing of heterochromatin proteins. Here, I outline the hallmarks of such transitions and the current challenges to detect them in living cells. I further discuss the abundance and properties of prominent heterochromatin proteins and relate them to their potential role in driving phase transitions. Recent data from mouse fibroblasts indicate that pericentric heterochromatin is organized via a reordering transition on the level of heterochromatin regions that does not necessarily involve liquid-liquid demixing of heterochromatin proteins. Evaluating key hallmarks of the different candidate phase transition mechanisms across cell types and species will be needed to complete the current picture.
Collapse
Affiliation(s)
- Fabian Erdel
- MCD, Center for Integrative Biology (CBI), CNRS, UPS, Toulouse, France.
| |
Collapse
|
36
|
Jedlička P, Tokan V, Kejnovská I, Hobza R, Kejnovský E. Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species. Mob DNA 2023; 14:3. [PMID: 37038191 PMCID: PMC10088271 DOI: 10.1186/s13100-023-00291-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Canonical telomeres (telomerase-synthetised) are readily forming G-quadruplexes (G4) on the G-rich strand. However, there are examples of non-canonical telomeres among eukaryotes where telomeric tandem repeats are invaded by specific retrotransposons. Drosophila melanogaster represents an extreme example with telomeres composed solely by three retrotransposons-Het-A, TAHRE and TART (HTT). Even though non-canonical telomeres often show strand biased G-distribution, the evidence for the G4-forming potential is limited. RESULTS Using circular dichroism spectroscopy and UV absorption melting assay we have verified in vitro G4-formation in the HTT elements of D. melanogaster. Namely 3 in Het-A, 8 in TART and 2 in TAHRE. All the G4s are asymmetrically distributed as in canonical telomeres. Bioinformatic analysis showed that asymmetric distribution of potential quadruplex sequences (PQS) is common in telomeric retrotransposons in other Drosophila species. Most of the PQS are located in the gag gene where PQS density correlates with higher DNA sequence conservation and codon selection favoring G4-forming potential. The importance of G4s in non-canonical telomeres is further supported by analysis of telomere-associated retrotransposons from various eukaryotic species including green algae, Diplomonadida, fungi, insects and vertebrates. Virtually all analyzed telomere-associated retrotransposons contained PQS, frequently with asymmetric strand distribution. Comparison with non-telomeric elements showed independent selection of PQS-rich elements from four distinct LINE clades. CONCLUSION Our findings of strand-biased G4-forming motifs in telomere-associated retrotransposons from various eukaryotic species support the G4-formation as one of the prerequisites for the recruitment of specific retrotransposons to chromosome ends and call for further experimental studies.
Collapse
Affiliation(s)
- Pavel Jedlička
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Viktor Tokan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic.
| | - Iva Kejnovská
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Eduard Kejnovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic.
| |
Collapse
|
37
|
Örkenby L, Skog S, Ekman H, Gozzo A, Kugelberg U, Ramesh R, Magadi S, Zambanini G, Nordin A, Cantú C, Nätt D, Öst A. Stress-sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis. Mol Syst Biol 2023; 19:e11148. [PMID: 36938679 PMCID: PMC10167479 DOI: 10.15252/msb.202211148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 02/15/2023] [Accepted: 02/23/2023] [Indexed: 03/21/2023] Open
Abstract
Early-life stress can result in life-long effects that impact adult health and disease risk, but little is known about how such programming is established and maintained. Here, we show that such epigenetic memories can be initiated in the Drosophila embryo before the major wave of zygotic transcription, and higher-order chromatin structures are established. An early short heat shock results in elevated levels of maternal miRNA and reduced levels of a subgroup of zygotic genes in stage 5 embryos. Using a Dicer-1 mutant, we show that the stress-induced decrease in one of these genes, the insulator-binding factor Elba1, is dependent on functional miRNA biogenesis. Reduction in Elba1 correlates with the upregulation of early developmental genes and promotes a sustained weakening of heterochromatin in the adult fly as indicated by an increased expression of the PEV wm4h reporter. We propose that maternal miRNAs, retained in response to an early embryonic heat shock, shape the subsequent de novo heterochromatin establishment that occurs during early development via direct or indirect regulation of some of the earliest expressed genes, including Elba1.
Collapse
Affiliation(s)
- Lovisa Örkenby
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Signe Skog
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Helen Ekman
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Alessandro Gozzo
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Unn Kugelberg
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Rashmi Ramesh
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Srivathsa Magadi
- Division of Neurobiology (NEURO), Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Division of Molecular Medicine and Virology (MMV), Linköping University, Linköping, Sweden
| | - Anna Nordin
- Division of Molecular Medicine and Virology (MMV), Linköping University, Linköping, Sweden
| | - Claudio Cantú
- Division of Molecular Medicine and Virology (MMV), Linköping University, Linköping, Sweden
| | - Daniel Nätt
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anita Öst
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| |
Collapse
|
38
|
Pecori F, Torres-Padilla ME. Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging. Dev Cell 2023; 58:435-449. [PMID: 36977375 PMCID: PMC10062924 DOI: 10.1016/j.devcel.2023.02.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/29/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023]
Abstract
Nuclear organization has emerged as a potential key regulator of genome function. During development, the deployment of transcriptional programs must be tightly coordinated with cell division and is often accompanied by major changes in the repertoire of expressed genes. These transcriptional and developmental events are paralleled by changes in the chromatin landscape. Numerous studies have revealed the dynamics of nuclear organization underlying them. In addition, advances in live-imaging-based methodologies enable the study of nuclear organization with high spatial and temporal resolution. In this Review, we summarize the current knowledge of the changes in nuclear architecture in the early embryogenesis of various model systems. Furthermore, to highlight the importance of integrating fixed-cell and live approaches, we discuss how different live-imaging techniques can be applied to examine nuclear processes and their contribution to our understanding of transcription and chromatin dynamics in early development. Finally, we provide future avenues for outstanding questions in this field.
Collapse
|
39
|
Shi Z, Xu J, Niu L, Shen W, Yan S, Tan Y, Quan X, Cheung E, Huang K, Chen Y, Li L, Hou C. Evolutionarily distinct and sperm-specific supersized chromatin loops are marked by Helitron transposons in Xenopus tropicalis. Cell Rep 2023; 42:112151. [PMID: 36827186 DOI: 10.1016/j.celrep.2023.112151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/24/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023] Open
Abstract
Transposable elements (TEs) are abundant in metazoan genomes and have multifaceted effects on host fitness. However, the mechanisms underlying the functions of TEs are still not fully understood. Here, we combine Hi-C, ATAC-seq, and ChIP-seq assays to report the existence of multimegabase supersized loop (SSL) clusters in the Xenopus tropicalis sperm. We show that SSL anchors are inaccessible and devoid of the architectural protein CTCF, RNA polymerase II, and modified histones. Nearly all SSL anchors are marked by Helitrons, a class II DNA transposon. Molecular dynamics simulations indicate that SSL clusters are likely formed via a molecular agent-mediated chromatin condensation process. However, only slightly more SSL anchor-associated genes are expressed at late embryo development stages, suggesting that SSL anchors might only function in sperm. Our work shows an evolutionarily distinct and sperm-specific genome structure marked by a subset of Helitrons, whose establishment and function remain to be explored.
Collapse
Affiliation(s)
- Zhaoying Shi
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jinsheng Xu
- Department of Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Longjian Niu
- China State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen 518055, China; Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei Shen
- Department of Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuting Yan
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yongjun Tan
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China; China State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xuebo Quan
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Edwin Cheung
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China; Frontier Science Centre for Precision Oncology of Ministry of Education, University of Macau, Taipa, Macau 999078, China
| | - Kai Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Yonglong Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Li Li
- Department of Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chunhui Hou
- China State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| |
Collapse
|
40
|
Li X, An Z, Zhang W, Li F. Phase Separation: Direct and Indirect Driving Force for High-Order Chromatin Organization. Genes (Basel) 2023; 14:499. [PMID: 36833426 PMCID: PMC9956262 DOI: 10.3390/genes14020499] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
The multi-level spatial chromatin organization in the nucleus is closely related to chromatin activity. The mechanism of chromatin organization and remodeling attract much attention. Phase separation describes the biomolecular condensation which is the basis for membraneless compartments in cells. Recent research shows that phase separation is a key aspect to drive high-order chromatin structure and remodeling. In addition, chromatin functional compartmentalization in the nucleus which is formed by phase separation also plays an important role in overall chromatin structure. In this review, we summarized the latest work about the role of phase separation in spatial chromatin organization, focusing on direct and indirect effects of phase separation on 3D chromatin organization and its impact on transcription regulation.
Collapse
Affiliation(s)
- Xiaoli Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
- Department of Cell Biology and Genetics, Core Facility of Developmental Biology, Chongqing Medical University, Chongqing 400016, China
| | - Ziyang An
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wenqing Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Feifei Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
| |
Collapse
|
41
|
Abstract
In animals, the sequences for controlling gene expression do not concentrate just at the transcription start site of genes, but are frequently thousands to millions of base pairs distal to it. The interaction of these sequences with one another and their transcription start sites is regulated by factors that shape the three-dimensional (3D) organization of the genome within the nucleus. Over the past decade, indirect tools exploiting high-throughput DNA sequencing have helped to map this 3D organization, have identified multiple key regulators of its structure and, in the process, have substantially reshaped our view of how 3D genome architecture regulates transcription. Now, new tools for high-throughput super-resolution imaging of chromatin have directly visualized the 3D chromatin organization, settling some debates left unresolved by earlier indirect methods, challenging some earlier models of regulatory specificity and creating hypotheses about the role of chromatin structure in transcriptional regulation.
Collapse
|
42
|
Cardamone F, Zhan Y, Iovino N, Zenk F. Chromosome Conformation Capture Followed by Genome-Wide Sequencing (Hi-C) in Drosophila Embryos. Methods Mol Biol 2023; 2655:41-55. [PMID: 37212987 DOI: 10.1007/978-1-0716-3143-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This protocol provides specific details on how to perform Hi-C, the genome-wide version of Chromosome Conformation Capture (3C) followed by high-throughput sequencing, in Drosophila embryos. Hi-C provides a genome-wide population-averaged snapshot of the 3D genome organization within nuclei. In Hi-C, formaldehyde-cross-linked chromatin is enzymatically digested using restriction enzymes; digested fragments are biotinylated and subjected to proximity ligation; ligated fragments are purified using streptavidin followed by paired-end sequencing. Hi-C allows the detection of higher order folding structures such as topologically associated domains (TADs) and active/inactive compartments (A/B compartments, respectively). Performing this assay in developing embryos gives the unique opportunity to investigate dynamic chromatin changes when 3D chromatin structure is established in embryogenesis.
Collapse
Affiliation(s)
- Francesco Cardamone
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- University of Freiburg, Faculty of Biology, Freiburg im Breisgau, Germany
| | - Yinxiu Zhan
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy.
| | - Nicola Iovino
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
| | - Fides Zenk
- Department of Biosystems Science and Engineering ETH (D-BSSE ETH Zürich), Basel, Switzerland.
| |
Collapse
|
43
|
Ling X, Liu X, Jiang S, Fan L, Ding J. The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:42. [PMID: 36539553 PMCID: PMC9768101 DOI: 10.1186/s13619-022-00145-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022]
Abstract
Cell fate transition is a fascinating process involving complex dynamics of three-dimensional (3D) chromatin organization and phase separation, which play an essential role in cell fate decision by regulating gene expression. Phase separation is increasingly being considered a driving force of chromatin folding. In this review, we have summarized the dynamic features of 3D chromatin and phase separation during physiological and pathological cell fate transitions and systematically analyzed recent evidence of phase separation facilitating the chromatin structure. In addition, we discuss current advances in understanding how phase separation contributes to physical and functional enhancer-promoter contacts. We highlight the functional roles of 3D chromatin organization and phase separation in cell fate transitions, and more explorations are required to study the regulatory relationship between 3D chromatin organization and phase separation. 3D chromatin organization (shown by Hi-C contact map) and phase separation are highly dynamic and play functional roles during early embryonic development, cell differentiation, somatic reprogramming, cell transdifferentiation and pathogenetic process. Phase separation can regulate 3D chromatin organization directly, but whether 3D chromatin organization regulates phase separation remains unclear.
Collapse
Affiliation(s)
- Xiaoru Ling
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Xinyi Liu
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Shaoshuai Jiang
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Lili Fan
- grid.258164.c0000 0004 1790 3548Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong China
| | - Junjun Ding
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.410737.60000 0000 8653 1072Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436 China ,grid.13291.380000 0001 0807 1581West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041 China
| |
Collapse
|
44
|
Di Stefano M, Cavalli G. Integrative studies of 3D genome organization and chromatin structure. Curr Opin Struct Biol 2022; 77:102493. [PMID: 36335845 DOI: 10.1016/j.sbi.2022.102493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
The structural organization of the genome is emerging as a crucial regulator of the cell state, affecting gene transcription, DNA replication, and repair. Over the last twenty years, increasing evidence prompted the development of new experimental techniques to study genome structure. In parallel with the complexity of the novel techniques, computational approaches have become an essential tool in any structural genomics laboratory to analyze and model the data. For biologists to be able to apply the most appropriate modeling approach, it is fundamental to understand the conceptual bases of distinct methods and the insights they can provide. Here, we will discuss recent advances that were possible thanks to 3D genome modeling, discuss their limitations and highlight future perspectives.
Collapse
Affiliation(s)
- Marco Di Stefano
- Institute of Human Genetics, CNRS and University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090, Montpellier, France. https://twitter.com/@MarcDiEsse
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090, Montpellier, France.
| |
Collapse
|
45
|
Lohia R, Fox N, Gillis J. A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships. Genome Biol 2022; 23:238. [PMID: 36352464 PMCID: PMC9647974 DOI: 10.1186/s13059-022-02790-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromatin contacts are essential for gene-expression regulation; however, obtaining a high-resolution genome-wide chromatin contact map is still prohibitively expensive owing to large genome sizes and the quadratic scale of pairwise data. Chromosome conformation capture (3C)-based methods such as Hi-C have been extensively used to obtain chromatin contacts. However, since the sparsity of these maps increases with an increase in genomic distance between contacts, long-range or trans-chromatin contacts are especially challenging to sample. RESULTS Here, we create a high-density reference genome-wide chromatin contact map using a meta-analytic approach. We integrate 3600 human, 6700 mouse, and 500 fly Hi-C experiments to create species-specific meta-Hi-C chromatin contact maps with 304 billion, 193 billion, and 19 billion contacts in respective species. We validate that meta-Hi-C contact maps are uniquely powered to capture functional chromatin contacts in both cis and trans. We find that while individual dataset Hi-C networks are largely unable to predict any long-range coexpression (median 0.54 AUC), meta-Hi-C networks perform comparably in both cis and trans (0.65 AUC vs 0.64 AUC). Similarly, for long-range expression quantitative trait loci (eQTL), meta-Hi-C contacts outperform all individual Hi-C experiments, providing an improvement over the conventionally used linear genomic distance-based association. Assessing between species, we find patterns of chromatin contact conservation in both cis and trans and strong associations with coexpression even in species for which Hi-C data is lacking. CONCLUSIONS We have generated an integrated chromatin interaction network which complements a large number of methodological and analytic approaches focused on improved specificity or interpretation. This high-depth "super-experiment" is surprisingly powerful in capturing long-range functional relationships of chromatin interactions, which are now able to predict coexpression, eQTLs, and cross-species relationships. The meta-Hi-C networks are available at https://labshare.cshl.edu/shares/gillislab/resource/HiC/ .
Collapse
Affiliation(s)
- Ruchi Lohia
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
| | - Nathan Fox
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
- Department of Physiology and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| |
Collapse
|
46
|
Sun M, Jiang W, Li X, Lee S, Heo G, Zhou D, Choi J, Kim K, Lv W, Cui X. ATF7-dependent epigenetic changes induced by high temperature during early porcine embryonic development. Cell Prolif 2022; 56:e13352. [PMID: 36254813 PMCID: PMC9890523 DOI: 10.1111/cpr.13352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/01/2022] [Accepted: 10/06/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Activating transcription factor 7 (ATF7) is a member of the ATF/cAMP response element (CRE) B superfamily. ATF2, ATF7, and CRE-BPa are present in vertebrates. Drosophila and fission yeast have only one homologue: dATF2 and Atf1, respectively. Under normal conditions, ATF7 promotes heterochromatin formation by recruiting histone H3K9 di- and tri-methyltransferases. Once the situation changes, all members are phosphorylated by the stress-activated kinase P38 in response to various stressors. However, the role of ATF7 in early porcine embryonic development remains unclear. RESULTS In this study, we found that ATF7 gradually accumulated in the nucleus and then localized on the pericentric heterochromatin after the late 4-cell stage, while being co-localized with heterochromatin protein 1 (HP1). Knockdown of ATF7 resulted in decreases in the blastocyst rate and blastocyst cell number. ATF7 depletion resulted in downregulation of HP1 and histone 3 lysine 9 dimethylation (H3K9me2) expression. These effects were alleviated when P38 activity was inhibited. High temperatures increased the expression level of pP38, while reducing the quality of porcine embryos, and led to ATF7 phosphorylation. The expression level of H3K9me2 and HP1 was decreased and regulated by P38 activity. CONCLUSION Stress-induced ATF7-dependent epigenetic changes play important roles in early porcine embryonic development.
Collapse
Affiliation(s)
- Ming‐Hong Sun
- Department of Animal ScienceChungbuk National UniversityCheongjuSouth Korea
| | - Wen‐Jie Jiang
- Department of Animal ScienceChungbuk National UniversityCheongjuSouth Korea
| | - Xiao‐Han Li
- Department of Animal ScienceChungbuk National UniversityCheongjuSouth Korea
| | - Song‐Hee Lee
- Department of Animal ScienceChungbuk National UniversityCheongjuSouth Korea
| | - Geun Heo
- Department of Animal ScienceChungbuk National UniversityCheongjuSouth Korea
| | - Dongjie Zhou
- Department of Animal ScienceChungbuk National UniversityCheongjuSouth Korea
| | - Jung‐Seok Choi
- Department of Animal ScienceChungbuk National UniversityCheongjuSouth Korea
| | - Kwan‐Suk Kim
- Department of Animal ScienceChungbuk National UniversityCheongjuSouth Korea
| | - Wenfa Lv
- College of Animal Science and TechnologyJilin Agricultural UniversityChangchunChina
| | - Xiang‐Shun Cui
- Department of Animal ScienceChungbuk National UniversityCheongjuSouth Korea
| |
Collapse
|
47
|
A Tremendous Reorganization Journey for the 3D Chromatin Structure from Gametes to Embryos. Genes (Basel) 2022; 13:genes13101864. [PMID: 36292750 PMCID: PMC9602195 DOI: 10.3390/genes13101864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 11/04/2022] Open
Abstract
The 3D chromatin structure within the nucleus is important for gene expression regulation and correct developmental programs. Recently, the rapid development of low-input chromatin conformation capture technologies has made it possible to study 3D chromatin structures in gametes, zygotes and early embryos in a variety of species, including flies, vertebrates and mammals. There are distinct 3D chromatin structures within the male and female gametes. Following the fertilization of male and female gametes, fertilized eggs undergo drastic epigenetic reprogramming at multi levels, including the 3D chromatin structure, to convert the terminally differentiated gamete state into the totipotent state, which can give rise to an individual. However, to what extent the 3D chromatin structure reorganization is evolutionarily conserved and what the underlying mechanisms are for the tremendous reorganization in early embryos remain elusive. Here, we review the latest findings on the 3D chromatin structure reorganization during embryogenesis, and discuss the convergent and divergent reprogramming patterns and key molecular mechanisms for the 3D chromatin structure reorganization from gametes to embryos in different species. These findings shed light on how the 3D chromatin structure reorganization contribute to embryo development in different species. The findings also indicate the role of the 3D chromatin structure on the acquisition of totipotent developmental potential.
Collapse
|
48
|
Cuartero S, Stik G, Stadhouders R. Three-dimensional genome organization in immune cell fate and function. Nat Rev Immunol 2022; 23:206-221. [PMID: 36127477 DOI: 10.1038/s41577-022-00774-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Immune cell development and activation demand the precise and coordinated control of transcriptional programmes. Three-dimensional (3D) organization of the genome has emerged as an important regulator of chromatin state, transcriptional activity and cell identity by facilitating or impeding long-range genomic interactions among regulatory elements and genes. Chromatin folding thus enables cell type-specific and stimulus-specific transcriptional responses to extracellular signals, which are essential for the control of immune cell fate, for inflammatory responses and for generating a diverse repertoire of antigen receptor specificities. Here, we review recent findings connecting 3D genome organization to the control of immune cell differentiation and function, and discuss how alterations in genome folding may lead to immune dysfunction and malignancy.
Collapse
Affiliation(s)
- Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain. .,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - Grégoire Stik
- Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands. .,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| |
Collapse
|
49
|
Singh PB, Newman AG. HP1-Driven Micro-Phase Separation of Heterochromatin-Like Domains/Complexes. Epigenet Insights 2022; 15:25168657221109766. [PMID: 35813402 PMCID: PMC9260563 DOI: 10.1177/25168657221109766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Prim B Singh
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan
| | - Andrew G Newman
- Institute of Cell and Neurobiology, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| |
Collapse
|
50
|
Haws SA, Simandi Z, Barnett RJ, Phillips-Cremins JE. 3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome. Cell 2022; 185:2690-2707. [PMID: 35868274 DOI: 10.1016/j.cell.2022.06.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 12/16/2022]
Abstract
Nearly half of the human genome is comprised of diverse repetitive sequences ranging from satellite repeats to retrotransposable elements. Such sequences are susceptible to stepwise expansions, duplications, inversions, and recombination events which can compromise genome function. In this review, we discuss the higher-order folding mechanisms of compartmentalization and loop extrusion and how they shape, and are shaped by, heterochromatin. Using primarily mammalian model systems, we contrast mechanisms governing H3K9me3-mediated heterochromatinization of the repetitive genome and highlight emerging links between repetitive elements and chromatin folding.
Collapse
Affiliation(s)
- Spencer A Haws
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoltan Simandi
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - R Jordan Barnett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|