1
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Puerto M, Shukla M, Bujosa P, Pérez-Roldán J, Torràs-Llort M, Tamirisa S, Carbonell A, Solé C, Puspo J, Cummings C, de Nadal E, Posas F, Azorín F, Rowley M. The zinc-finger protein Z4 cooperates with condensin II to regulate somatic chromosome pairing and 3D chromatin organization. Nucleic Acids Res 2024; 52:5596-5609. [PMID: 38520405 PMCID: PMC11162801 DOI: 10.1093/nar/gkae198] [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: 10/24/2023] [Revised: 02/16/2024] [Accepted: 03/07/2024] [Indexed: 03/25/2024] Open
Abstract
Chromosome pairing constitutes an important level of genome organization, yet the mechanisms that regulate pairing in somatic cells and the impact on 3D chromatin organization are still poorly understood. Here, we address these questions in Drosophila, an organism with robust somatic pairing. In Drosophila, pairing preferentially occurs at loci consisting of numerous architectural protein binding sites (APBSs), suggesting a role of architectural proteins (APs) in pairing regulation. Amongst these, the anti-pairing function of the condensin II subunit CAP-H2 is well established. However, the factors that regulate CAP-H2 localization and action at APBSs remain largely unknown. Here, we identify two factors that control CAP-H2 occupancy at APBSs and, therefore, regulate pairing. We show that Z4, interacts with CAP-H2 and is required for its localization at APBSs. We also show that hyperosmotic cellular stress induces fast and reversible unpairing in a Z4/CAP-H2 dependent manner. Moreover, by combining the opposite effects of Z4 depletion and osmostress, we show that pairing correlates with the strength of intrachromosomal 3D interactions, such as active (A) compartment interactions, intragenic gene-loops, and polycomb (Pc)-mediated chromatin loops. Altogether, our results reveal new players in CAP-H2-mediated pairing regulation and the intimate interplay between inter-chromosomal and intra-chromosomal 3D interactions.
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Affiliation(s)
- Marta Puerto
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Mamta Shukla
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Paula Bujosa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Juan Pérez-Roldán
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Mònica Torràs-Llort
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Srividya Tamirisa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Albert Carbonell
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Carme Solé
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Joynob Akter Puspo
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Eulàlia de Nadal
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesc Posas
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
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2
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Li J, Lin Y, Li D, He M, Kui H, Bai J, Chen Z, Gou Y, Zhang J, Wang T, Tang Q, Kong F, Jin L, Li M. Building Haplotype-Resolved 3D Genome Maps of Chicken Skeletal Muscle. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305706. [PMID: 38582509 PMCID: PMC11200017 DOI: 10.1002/advs.202305706] [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: 08/15/2023] [Revised: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Haplotype-resolved 3D chromatin architecture related to allelic differences in avian skeletal muscle development has not been addressed so far, although chicken husbandry for meat consumption has been prevalent feature of cultures on every continent for more than thousands of years. Here, high-resolution Hi-C diploid maps (1.2-kb maximum resolution) are generated for skeletal muscle tissues in chicken across three developmental stages (embryonic day 15 to day 30 post-hatching). The sequence features governing spatial arrangement of chromosomes and characterize homolog pairing in the nucleus, are identified. Multi-scale characterization of chromatin reorganization between stages from myogenesis in the fetus to myofiber hypertrophy after hatching show concordant changes in transcriptional regulation by relevant signaling pathways. Further interrogation of parent-of-origin-specific chromatin conformation supported that genomic imprinting is absent in birds. This study also reveals promoter-enhancer interaction (PEI) differences between broiler and layer haplotypes in skeletal muscle development-related genes are related to genetic variation between breeds, however, only a minority of breed-specific variations likely contribute to phenotypic divergence in skeletal muscle potentially via allelic PEI rewiring. Beyond defining the haplotype-specific 3D chromatin architecture in chicken, this study provides a rich resource for investigating allelic regulatory divergence among chicken breeds.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Yu Lin
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Diyan Li
- School of PharmacyChengdu UniversityChengdu610106China
| | - Mengnan He
- Wildlife Conservation Research DepartmentChengdu Research Base of Giant Panda BreedingChengdu610057China
| | - Hua Kui
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Jingyi Bai
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Ziyu Chen
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Yuwei Gou
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Tao Wang
- School of PharmacyChengdu UniversityChengdu610106China
| | - Qianzi Tang
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Fanli Kong
- College of Life ScienceSichuan Agricultural UniversityYa'an625014China
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
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3
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Lee L, Rosin LF. Uncharted territories: Solving the mysteries of male meiosis in flies. PLoS Genet 2024; 20:e1011185. [PMID: 38489251 PMCID: PMC10942038 DOI: 10.1371/journal.pgen.1011185] [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] [Indexed: 03/17/2024] Open
Abstract
The segregation of homologous chromosomes during meiosis typically requires tight end-to-end chromosome pairing. However, in Drosophila spermatogenesis, male flies segregate their chromosomes without classic synaptonemal complex formation and without recombination, instead compartmentalizing homologs into subnuclear domains known as chromosome territories (CTs). How homologs find each other in the nucleus and are separated into CTs has been one of the biggest riddles in chromosome biology. Here, we discuss our current understanding of pairing and CT formation in flies and review recent data on how homologs are linked and partitioned during meiosis in male flies.
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Affiliation(s)
- LingSze Lee
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Leah F. Rosin
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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4
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Abstract
Many cellular processes require large-scale rearrangements of chromatin structure. Structural maintenance of chromosomes (SMC) protein complexes are molecular machines that can provide structure to chromatin. These complexes can connect DNA elements in cis, walk along DNA, build and processively enlarge DNA loops and connect DNA molecules in trans to hold together the sister chromatids. These DNA-shaping abilities place SMC complexes at the heart of many DNA-based processes, including chromosome segregation in mitosis, transcription control and DNA replication, repair and recombination. In this Review, we discuss the latest insights into how SMC complexes such as cohesin, condensin and the SMC5-SMC6 complex shape DNA to direct these fundamental chromosomal processes. We also consider how SMC complexes, by building chromatin loops, can counteract the natural tendency of alike chromatin regions to cluster. SMC complexes thus control nuclear organization by participating in a molecular tug of war that determines the architecture of our genome.
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Affiliation(s)
- Claire Hoencamp
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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5
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Jia BB, Jussila A, Kern C, Zhu Q, Ren B. A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nat Biotechnol 2023; 41:1004-1017. [PMID: 36593410 PMCID: PMC10344783 DOI: 10.1038/s41587-022-01568-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 10/13/2022] [Indexed: 01/03/2023]
Abstract
Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.
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Affiliation(s)
- Bojing Blair Jia
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
- Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
| | - Adam Jussila
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Colin Kern
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Quan Zhu
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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6
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Puerto M, Shukla M, Bujosa P, Perez-Roldan J, Tamirisa S, Solé C, de Nadal E, Posas F, Azorin F, Rowley MJ. Somatic chromosome pairing has a determinant impact on 3D chromatin organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534693. [PMID: 37034722 PMCID: PMC10081234 DOI: 10.1101/2023.03.29.534693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
In the nucleus, chromatin is intricately structured into multiple layers of 3D organization important for genome activity. How distinct layers influence each other is not well understood. In particular, the contribution of chromosome pairing to 3D chromatin organization has been largely neglected. Here, we address this question in Drosophila, an organism that shows robust chromosome pairing in interphasic somatic cells. The extent of chromosome pairing depends on the balance between pairing and anti-pairing factors, with the anti-pairing activity of the CAP-H2 condensin II subunit being the best documented. Here, we identify the zinc-finger protein Z4 as a strong anti-pairer that interacts with and mediates the chromatin binding of CAP-H2. We also report that hyperosmotic cellular stress induces fast and reversible chromosome unpairing that depends on Z4/CAP-H2. And, most important, by combining Z4 depletion and osmostress, we show that chromosome pairing reinforces intrachromosomal 3D interactions. On the one hand, pairing facilitates RNAPII occupancy that correlates with enhanced intragenic gene-loop interactions. In addition, acting at a distance, pairing reinforces chromatin-loop interactions mediated by Polycomb (Pc). In contrast, chromosome pairing does not affect which genomic intervals segregate to active (A) and inactive (B) compartments, with only minimal effects on the strength of A-A compartmental interactions. Altogether, our results unveil the intimate interplay between inter-chromosomal and intra-chromosomal 3D interactions, unraveling the interwoven relationship between different layers of chromatin organization and the essential contribution of chromosome pairing.
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7
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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.
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8
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Mazur AK, Gladyshev E. C-DNA may facilitate homologous DNA pairing. Trends Genet 2023:S0168-9525(23)00023-9. [PMID: 36804168 DOI: 10.1016/j.tig.2023.01.008] [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: 10/25/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
Recombination-independent homologous pairing represents a prominent yet largely enigmatic feature of chromosome biology. As suggested by studies in the fungus Neurospora crassa, this process may be based on the direct pairing of homologous DNA molecules. Theoretical search for the DNA structures consistent with those genetic results has led to an all-atom model in which the B-DNA conformation of the paired double helices is strongly shifted toward C-DNA. Coincidentally, C-DNA also features a very shallow major groove that could permit initial homologous contacts without atom-atom clashes. The hereby conjectured role of C-DNA in homologous pairing should encourage the efforts to discover its biological functions and may also clarify the mechanism of recombination-independent recognition of DNA homology.
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Affiliation(s)
- Alexey K Mazur
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, Paris, France; Institut Pasteur, Université Paris Cité, Group Fungal Epigenomics, Paris, France.
| | - Eugene Gladyshev
- Institut Pasteur, Université Paris Cité, Group Fungal Epigenomics, Paris, France.
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9
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Rzezniczak TZ, Rzezniczak MT, Reed BH, Dworkin I, Merritt TJS. Regulation at Drosophila's Malic Enzyme highlights the complexity of transvection and its sensitivity to genetic background. Genetics 2022; 223:6884207. [PMID: 36482767 PMCID: PMC9910402 DOI: 10.1093/genetics/iyac181] [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: 10/12/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Transvection, a type of trans-regulation of gene expression in which regulatory elements on one chromosome influence elements on a paired homologous chromosome, is itself a complex biological phenotype subject to modification by genetic background effects. However, relatively few studies have explored how transvection is affected by distal genetic variation, perhaps because it is strongly influenced by local regulatory elements and chromosomal architecture. With the emergence of the "hub" model of transvection and a series of studies showing variation in transvection effects, it is becoming clear that genetic background plays an important role in how transvection influences gene transcription. We explored the effects of genetic background on transvection by performing two independent genome wide association studies (GWASs) using the Drosophila genetic reference panel (DGRP) and a suite of Malic enzyme (Men) excision alleles. We found substantial variation in the amount of transvection in the 149 DGRP lines used, with broad-sense heritability of 0.89 and 0.84, depending on the excision allele used. The specific genetic variation identified was dependent on the excision allele used, highlighting the complex genetic interactions influencing transvection. We focussed primarily on genes identified as significant using a relaxed P-value cutoff in both GWASs. The most strongly associated genetic variant mapped to an intergenic single nucleotide polymorphism (SNP), located upstream of Tiggrin (Tig), a gene that codes for an extracellular matrix protein. Variants in other genes, such transcription factors (CG7368 and Sima), RNA binding proteins (CG10418, Rbp6, and Rig), enzymes (AdamTS-A, CG9743, and Pgant8), proteins influencing cell cycle progression (Dally and Eip63E) and signaling proteins (Atg-1, Axo, Egfr, and Path) also associated with transvection in Men. Although not intuitively obvious how many of these genes may influence transvection, some have been previously identified as promoting or antagonizing somatic homolog pairing. These results identify several candidate genes to further explore in the understanding of transvection in Men and in other genes regulated by transvection. Overall, these findings highlight the complexity of the interactions involved in gene regulation, even in phenotypes, such as transvection, that were traditionally considered to be primarily influenced by local genetic variation.
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Affiliation(s)
- Teresa Z Rzezniczak
- Department of Chemistry & Biochemistry, Laurentian University, Sudbury, ON P3E 2C6, Canada
| | - Mark T Rzezniczak
- Department of Chemistry & Biochemistry, Laurentian University, Sudbury, ON P3E 2C6, Canada
| | - Bruce H Reed
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Ian Dworkin
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Thomas J S Merritt
- Corresponding author: Department of Chemistry & Biochemistry, Laurentian University, Sudbury, ON P3E 2C6, Canada.
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10
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Azeroglu B, Ozbun L, Pegoraro G, Lazzerini Denchi E. Native FISH: A low- and high-throughput assay to analyze the alternative lengthening of telomere (ALT) pathway. Methods Cell Biol 2022; 182:265-284. [PMID: 38359982 DOI: 10.1016/bs.mcb.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a telomerase-independent and recombination-based mechanism used by approximately 15% of human cancers to maintain telomere length and to sustain proliferation. ALT-positive cells display unique features that could be exploited for tailored cancer therapies. A key limitation for the development of ALT-specific treatments is the lack of an assay to detect ALT-positive cells that is easy to perform and that can be scaled up. One of the most broadly used assays for ALT detection, CCA (C-circle assay), does not provide single-cell information and it is not amenable to High-Throughput Screening (HTS). To overcome these limitations, we developed Native-FISH (N-FISH) as an alternative method to visualize ALT-specific single-stranded telomeric DNA. N-FISH produces single-cell data, can be applied to fixed tissues, does not require DNA isolation or amplification steps, and it can be miniaturized in a 384-well format. This protocol details the steps to perform N-FISH protocol both in a low- and high-throughput format to analyze ALT. While low-throughput N-FISH is useful to assay the ALT state of cell lines, we expect that the miniaturized N-FISH assay coupled with high-throughput imaging will be useful in functional genomics and chemical screens to identify novel cellular factors that regulate ALT and potential ALT therapeutic targets for cancer therapies directed against ALT-positive tumors, respectively.
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Affiliation(s)
- Benura Azeroglu
- Laboratory of Genome Integrity, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States.
| | - Laurent Ozbun
- High-Throughput Imaging Facility (HiTIF), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Eros Lazzerini Denchi
- Laboratory of Genome Integrity, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
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11
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Goupil A, Heinen JP, Salame R, Rossi F, Reina J, Pennetier C, Simon A, Skorski P, Louzao A, Bardin AJ, Basto R, Gonzalez C. Illuminati: a form of gene expression plasticity in Drosophila neural stem cells. Development 2022; 149:282932. [PMID: 36399062 PMCID: PMC9845751 DOI: 10.1242/dev.200808] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/06/2022] [Indexed: 11/21/2022]
Abstract
While testing for genome instability in Drosophila as reported by unscheduled upregulation of UAS-GFP in cells that co-express GAL80 and GAL4, we noticed that, as expected, background levels were low in most developing tissues. However, GFP-positive clones were frequent in the larval brain. Most of these clones originated from central brain neural stem cells. Using imaging-based approaches and genome sequencing, we show that these unscheduled clones do not result from chromosome loss or mutations in GAL80. We have named this phenomenon 'Illuminati'. Illuminati is strongly enhanced in brat tumors and is also sensitive to environmental conditions such as food content and temperature. Illuminati is suppressed by Su(var)2-10, but it is not significantly affected by several modifiers of position effect variegation or Gal4::UAS variegation. We conclude that Illuminati identifies a previously unknown type of functional instability that may have important implications in development and disease.
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Affiliation(s)
- Alix Goupil
- Institut Curie, Paris Science et Lettres Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche UMR144, Biology of Centrosomes and Genetic Instability Laboratory, 75005 Paris, France
| | - Jan Peter Heinen
- Institute for Research in Biomedicine (IRB Barcelona), Cell Division Laboratory, Cancer Science Programme, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Riham Salame
- Institut Curie, Paris Science et Lettres Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche UMR144, Biology of Centrosomes and Genetic Instability Laboratory, 75005 Paris, France
| | - Fabrizio Rossi
- Institute for Research in Biomedicine (IRB Barcelona), Cell Division Laboratory, Cancer Science Programme, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jose Reina
- Institute for Research in Biomedicine (IRB Barcelona), Cell Division Laboratory, Cancer Science Programme, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Carole Pennetier
- Institut Curie, Paris Science et Lettres Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche UMR144, Biology of Centrosomes and Genetic Instability Laboratory, 75005 Paris, France
| | - Anthony Simon
- Institut Curie, Paris Science et Lettres Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche UMR144, Biology of Centrosomes and Genetic Instability Laboratory, 75005 Paris, France
| | - Patricia Skorski
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
| | - Anxela Louzao
- Institute for Research in Biomedicine (IRB Barcelona), Cell Division Laboratory, Cancer Science Programme, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Allison J. Bardin
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
| | - Renata Basto
- Institut Curie, Paris Science et Lettres Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche UMR144, Biology of Centrosomes and Genetic Instability Laboratory, 75005 Paris, France,Authors for correspondence (; )
| | - Cayetano Gonzalez
- Institute for Research in Biomedicine (IRB Barcelona), Cell Division Laboratory, Cancer Science Programme, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain,Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain,Authors for correspondence (; )
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12
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Fleck K, Raj R, Erceg J. The 3D genome landscape: Diverse chromosomal interactions and their functional implications. Front Cell Dev Biol 2022; 10:968145. [PMID: 36036013 PMCID: PMC9402908 DOI: 10.3389/fcell.2022.968145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Genome organization includes contacts both within a single chromosome and between distinct chromosomes. Thus, regulatory organization in the nucleus may include interplay of these two types of chromosomal interactions with genome activity. Emerging advances in omics and single-cell imaging technologies have allowed new insights into chromosomal contacts, including those of homologs and sister chromatids, and their significance to genome function. In this review, we highlight recent studies in this field and discuss their impact on understanding the principles of chromosome organization and associated functional implications in diverse cellular processes. Specifically, we describe the contributions of intra-chromosomal, inter-homolog, and inter-sister chromatid contacts to genome organization and gene expression.
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Affiliation(s)
- Katherine Fleck
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Romir Raj
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Jelena Erceg
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, United States
- *Correspondence: Jelena Erceg,
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13
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Voortman L, Anderson C, Urban E, Yuan L, Tran S, Neuhaus-Follini A, Derrick J, Gregor T, Johnston RJ. Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. Dev Cell 2022; 57:1817-1832.e5. [PMID: 35835116 PMCID: PMC9378680 DOI: 10.1016/j.devcel.2022.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 01/12/2023]
Abstract
Stochastic mechanisms diversify cell fates during development. How cells randomly choose between two or more fates remains poorly understood. In the Drosophila eye, the random mosaic of two R7 photoreceptor subtypes is determined by expression of the transcription factor Spineless (Ss). We investigated how cis-regulatory elements and trans factors regulate nascent transcriptional activity and chromatin compaction at the ss gene locus during R7 development. The ss locus is in a compact state in undifferentiated cells. An early enhancer drives transcription in all R7 precursors, and the locus opens. In differentiating cells, transcription ceases and the ss locus stochastically remains open or compacts. In SsON R7s, ss is open and competent for activation by a late enhancer, whereas in SsOFF R7s, ss is compact, and repression prevents expression. Our results suggest that a temporally dynamic antagonism, in which transcription drives large-scale decompaction and then compaction represses transcription, controls stochastic fate specification.
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Affiliation(s)
- Lukas Voortman
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Caitlin Anderson
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Urban
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Luorongxin Yuan
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sang Tran
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Josh Derrick
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Joseph Henry Laboratories of Physics, the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Developmental and Stem Cell Biology, UMR3738, Institut Pasteur, 75015 Paris, France
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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14
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Gantz VM, Bier E. Active genetics comes alive: Exploring the broad applications of CRISPR-based selfish genetic elements (or gene-drives): Exploring the broad applications of CRISPR-based selfish genetic elements (or gene-drives). Bioessays 2022; 44:e2100279. [PMID: 35686327 PMCID: PMC9397133 DOI: 10.1002/bies.202100279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/11/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based "active genetic" elements developed in 2015 bypassed the fundamental rules of traditional genetics. Inherited in a super-Mendelian fashion, such selfish genetic entities offered a variety of potential applications including: gene-drives to disseminate gene cassettes carrying desired traits throughout insect populations to control disease vectors or pest species, allelic drives biasing inheritance of preferred allelic variants, neutralizing genetic elements to delete and replace or to halt the spread of gene-drives, split-drives with the core constituent Cas9 endonuclease and guide RNA (gRNA) components inserted at separate genomic locations to accelerate assembly of complex arrays of genetic traits or to gain genetic entry into novel organisms (vertebrates, plants, bacteria), and interhomolog based copying systems in somatic cells to develop tools for treating inherited or infectious diseases. Here, we summarize the substantial advances that have been made on all of these fronts and look forward to the next phase of this rapidly expanding and impactful field.
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Affiliation(s)
- Valentino M Gantz
- Department of Cell and Developmental Biology, University of California, La Jolla, California, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, La Jolla, California, USA
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15
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Antel M, Raj R, Masoud MYG, Pan Z, Li S, Mellone BG, Inaba M. Interchromosomal interaction of homologous Stat92E alleles regulates transcriptional switch during stem-cell differentiation. Nat Commun 2022; 13:3981. [PMID: 35810185 PMCID: PMC9271046 DOI: 10.1038/s41467-022-31737-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 06/30/2022] [Indexed: 01/24/2023] Open
Abstract
Pairing of homologous chromosomes in somatic cells provides the opportunity of interchromosomal interaction between homologous gene regions. In the Drosophila male germline, the Stat92E gene is highly expressed in a germline stem cell (GSC) and gradually downregulated during the differentiation. Here we show that the pairing of Stat92E is always tight in GSCs and immediately loosened in differentiating daughter cells, gonialblasts (GBs). Disturbance of Stat92E pairing by relocation of one locus to another chromosome or by knockdown of global pairing/anti-pairing factors both result in a failure of Stat92E downregulation, suggesting that the pairing is required for the decline in transcription. Furthermore, the Stat92E enhancer, but not its transcription, is required for the change in pairing state, indicating that pairing is not a consequence of transcriptional changes. Finally, we show that the change in Stat92E pairing is dependent on asymmetric histone inheritance during the asymmetric division of GSCs. Taken together, we propose that the changes in Stat92E pairing status is an intrinsically programmed mechanism for enabling prompt cell fate switch during the differentiation of stem cells. Asymmetric inheritance of organelles, proteins and RNAs occurs during stem cell division. Here the authors show the strength of pairing of homologous Stat92E loci, a stem cell-specific gene, changes immediately after the asymmetric division due to asymmetric inheritance of new histones to one of the daughter cells and is important for turning off gene expression in this cell as it differentiates.
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Affiliation(s)
- Matthew Antel
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Romir Raj
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Madona Y G Masoud
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Ziwei Pan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Department of Genetics and Genomic Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Department of Genetics and Genomic Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Barbara G Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Mayu Inaba
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA.
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16
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Bateman JR, Johnson JE. Altering enhancer-promoter linear distance impacts promoter competition in cis and in trans. Genetics 2022; 222:6617354. [PMID: 35748724 PMCID: PMC9434180 DOI: 10.1093/genetics/iyac098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/18/2022] [Indexed: 11/14/2022] Open
Abstract
In Drosophila, pairing of maternal and paternal homologs can permit trans-interactions between enhancers on one homolog and promoters on another, an example of a phenomenon called transvection. When chromosomes are paired, promoters in cis and in trans to an enhancer can compete for the enhancer's activity, but the parameters that govern this competition are as yet poorly understood. To assess how the linear spacing between an enhancer and promoter can influence promoter competition in Drosophila, we employed transgenic constructs wherein the eye-specific enhancer GMR is placed at varying distances from a heterologous hsp70 promoter driving a fluorescent reporter. While GMR activates the reporter to a high degree when the enhancer and promoter are spaced by a few hundred base pairs, activation is strongly attenuated when the enhancer is moved 3 kilobases away. By examining transcription of endogenous genes near the point of transgene insertion, we show that linear spacing of 3 kb between GMR and the hsp70 promoter results in elevated transcription of neighboring promoters, suggesting a loss of specificity between the enhancer and its intended transgenic target promoter. Furthermore, increasing spacing between GMR and hsp70 by just 100 bp can enhance transvection, resulting in increased activation of a promoter on a paired homolog at the expense of a promoter in cis to the enhancer. Finally, cis-/trans-promoter competition assays in which one promoter carries mutations to key core promoter elements show that GMR will skew its activity toward a wild type promoter, suggesting that an enhancer is in a balanced competition between its potential target promoters in cis and in trans.
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Affiliation(s)
- Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
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17
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Brahmachari S, Contessoto VG, Di Pierro M, Onuchic JN. Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion. Nucleic Acids Res 2022; 50:4258-4271. [PMID: 35420130 PMCID: PMC9071446 DOI: 10.1093/nar/gkac231] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/02/2022] [Accepted: 04/11/2022] [Indexed: 01/13/2023] Open
Abstract
The link between genomic structure and biological function is yet to be consolidated, it is, however, clear that physical manipulation of the genome, driven by the activity of a variety of proteins, is a crucial step. To understand the consequences of the physical forces underlying genome organization, we build a coarse-grained polymer model of the genome, featuring three fundamentally distinct classes of interactions: lengthwise compaction, i.e., compaction of chromosomes along its contour, self-adhesion among epigenetically similar genomic segments, and adhesion of chromosome segments to the nuclear envelope or lamina. We postulate that these three types of interactions sufficiently represent the concerted action of the different proteins organizing the genome architecture and show that an interplay among these interactions can recapitulate the architectural variants observed across the tree of life. The model elucidates how an interplay of forces arising from the three classes of genomic interactions can drive drastic, yet predictable, changes in the global genome architecture, and makes testable predictions. We posit that precise control over these interactions in vivo is key to the regulation of genome architecture.
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Affiliation(s)
| | | | - Michele Di Pierro
- Department of Physics, and Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.,Department of Physics and Astronomy, Department of Chemistry, Department of BioSciences, Rice University, Houston TX 77005, USA
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18
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El Dika M, Fritz AJ, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Fidelity of Mechanisms Governing the Cell Cycle. Results Probl Cell Differ 2022; 70:375-396. [PMID: 36348115 PMCID: PMC9703624 DOI: 10.1007/978-3-031-06573-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cell cycle is governed by stringent epigenetic mechanisms that, in response to intrinsic and extrinsic regulatory cues, support fidelity of DNA replication and cell division. We will focus on (1) the complex and interdependent processes that are obligatory for control of proliferation and compromised in cancer, (2) epigenetic and topological domains that are associated with distinct phases of the cell cycle that may be altered in cancer initiation and progression, and (3) the requirement for mitotic bookmarking to maintain intranuclear localization of transcriptional regulatory machinery to reinforce cell identity throughout the cell cycle to prevent malignant transformation.
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Affiliation(s)
- Mohammed El Dika
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Andrew J. Fritz
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rabail H. Toor
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | | | - Stephen J. Foley
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rahim Ullah
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Daijing Nie
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Bodhisattwa Banerjee
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Dorcas Lohese
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Karen C. Glass
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Pharmacology, Burlington, VT 05405
| | - Seth Frietze
- University of Vermont, College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jessica L. Heath
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405,University of Vermont, Larner College of Medicine, Department of Pediatrics, Burlington, VT 05405
| | - Anthony N. Imbalzano
- UMass Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester, MA 01605
| | - Andre van Wijnen
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jonathan Gordon
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jane B. Lian
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Janet L. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Gary S. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
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19
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Hua LL, Casas C, Mikawa T. Mitotic Antipairing of Homologous Chromosomes. Results Probl Cell Differ 2022; 70:191-220. [PMID: 36348108 PMCID: PMC9731508 DOI: 10.1007/978-3-031-06573-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromosome organization is highly dynamic and plays an essential role during cell function. It was recently found that pairs of the homologous chromosomes are continuously separated at mitosis and display a haploid (1n) chromosome set, or "antipairing," organization in human cells. Here, we provide an introduction to the current knowledge of homologous antipairing in humans and its implications in human disease.
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Affiliation(s)
- Lisa L. Hua
- Department of Biology, Sonoma State University, San Francisco
| | - Christian Casas
- Department of Biology, Sonoma State University, San Francisco
| | - Takashi Mikawa
- Department of Anatomy, Cardiovascular Research Institute, University of California, San Francisco,Corresponding author:
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20
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Abstract
High-throughput DNA fluorescence in situ hybridization (hiFISH) combines multicolor combinatorial DNA FISH staining with automated image acquisition and analysis to visualize and localize tens to hundreds of genomic loci in up to millions of cells. hiFISH can be used to measure physical distances between pairs of genomic loci, radial distances from genomic loci to the nuclear edge or center, and distances between genomic loci and nuclear structures defined by protein or RNA markers. The resulting large datasets of 3D spatial distances can be used to study cellular heterogeneity in genome architecture and the molecular mechanisms underlying this phenomenon in a variety of cellular systems. In this chapter we provide detailed protocols for hiFISH to measure distances between genomic loci, including all steps involved in DNA FISH probe design and preparation, cell culture, DNA FISH staining in 384-well imaging plates, automated image acquisition and analysis, and, finally, statistical analysis.
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Affiliation(s)
- Elizabeth Finn
- Cell Biology of Genomes (CBGE), Center for Cancer Research (CCR), NCI/NIH, Bethesda, MD, USA.
| | - Tom Misteli
- Cell Biology of Genomes (CBGE), Center for Cancer Research (CCR), NCI/NIH, Bethesda, MD, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), NCI/NIH, Bethesda, MD, USA.
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21
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Galouzis CC, Prud’homme B. Relevance and mechanisms of transvection. C R Biol 2021; 344:373-387. [DOI: 10.5802/crbiol.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 11/24/2022]
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22
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Carlier F, Nguyen TS, Mazur AK, Gladyshev E. Modulation of C-to-T mutation by recombination-independent pairing of closely positioned DNA repeats. Biophys J 2021; 120:4325-4336. [PMID: 34509507 DOI: 10.1016/j.bpj.2021.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/14/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022] Open
Abstract
Repeat-induced point mutation is a genetic process that creates cytosine-to-thymine (C-to-T) transitions in duplicated genomic sequences in fungi. Repeat-induced point mutation detects duplications (irrespective of their origin, specific sequence, coding capacity, and genomic positions) by a recombination-independent mechanism that likely matches intact DNA double helices directly, without relying on the annealing of complementary single strands. In the fungus Neurospora crassa, closely positioned repeats can induce mutation of the adjoining nonrepetitive regions. This process is related to heterochromatin assembly and requires the cytosine methyltransferase DIM-2. Using DIM-2-dependent mutation as a readout of homologous pairing, we find that GC-rich repeats produce a much stronger response than AT-rich repeats, independently of their intrinsic propensity to become mutated. We also report that direct repeats trigger much stronger DIM-2-dependent mutation than inverted repeats. These results can be rationalized in the light of a recently proposed model of homologous DNA pairing, in which DNA double helices associate by forming sequence-specific quadruplex-based contacts with a concomitant release of supercoiling. A similar process featuring pairing-induced supercoiling may initiate epigenetic silencing of repetitive DNA in other organisms, including humans.
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Affiliation(s)
- Florian Carlier
- Group "Fungal Epigenomics", Department of Mycology, Institut Pasteur, Paris, France
| | - Tinh-Suong Nguyen
- Group "Fungal Epigenomics", Department of Mycology, Institut Pasteur, Paris, France
| | - Alexey K Mazur
- Group "Fungal Epigenomics", Department of Mycology, Institut Pasteur, Paris, France; CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France.
| | - Eugene Gladyshev
- Group "Fungal Epigenomics", Department of Mycology, Institut Pasteur, Paris, France.
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23
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Vernizzi L, Lehner CF. Bivalent individualization during chromosome territory formation in Drosophila spermatocytes by controlled condensin II protein activity and additional force generators. PLoS Genet 2021; 17:e1009870. [PMID: 34669718 PMCID: PMC8559962 DOI: 10.1371/journal.pgen.1009870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/01/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
Reduction of genome ploidy from diploid to haploid necessitates stable pairing of homologous chromosomes into bivalents before the start of the first meiotic division. Importantly, this chromosome pairing must avoid interlocking of non-homologous chromosomes. In spermatocytes of Drosophila melanogaster, where homolog pairing does not involve synaptonemal complex formation and crossovers, associations between non-homologous chromosomes are broken up by chromosome territory formation in early spermatocytes. Extensive non-homologous associations arise from the coalescence of the large blocks of pericentromeric heterochromatin into a chromocenter and from centromere clustering. Nevertheless, during territory formation, bivalents are moved apart into spatially separate subnuclear regions. The condensin II subunits, Cap-D3 and Cap-H2, have been implicated, but the remarkable separation of bivalents during interphase might require more than just condensin II. For further characterization of this process, we have applied time-lapse imaging using fluorescent markers of centromeres, telomeres and DNA satellites in pericentromeric heterochromatin. We describe the dynamics of the disruption of centromere clusters and the chromocenter in normal spermatocytes. Mutations in Cap-D3 and Cap-H2 abolish chromocenter disruption, resulting in excessive chromosome missegregation during M I. Chromocenter persistence in the mutants is not mediated by the special system, which conjoins homologs in compensation for the absence of crossovers in Drosophila spermatocytes. However, overexpression of Cap-H2 precluded conjunction between autosomal homologs, resulting in random segregation of univalents. Interestingly, Cap-D3 and Cap-H2 mutant spermatocytes displayed conspicuous stretching of the chromocenter, as well as occasional chromocenter disruption, suggesting that territory formation might involve forces unrelated to condensin II. While the molecular basis of these forces remains to be clarified, they are not destroyed by inhibitors of F actin and microtubules. Our results indicate that condensin II activity promotes chromosome territory formation in co-operation with additional force generators and that careful co-ordination with alternative homolog conjunction is crucial.
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Affiliation(s)
- Luisa Vernizzi
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
| | - Christian F. Lehner
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
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24
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Liu Y, Zhao N, Kanemaki MT, Yamamoto Y, Sadamura Y, Ito Y, Tokunaga M, Stasevich TJ, Kimura H. Visualizing looping of two endogenous genomic loci using synthetic zinc-finger proteins with anti-FLAG and anti-HA frankenbodies in living cells. Genes Cells 2021; 26:905-926. [PMID: 34465007 PMCID: PMC8893316 DOI: 10.1111/gtc.12893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/17/2022]
Abstract
In eukaryotic nuclei, chromatin loops mediated through cohesin are critical structures that regulate gene expression and DNA replication. Here, we demonstrate a new method to see endogenous genomic loci using synthetic zinc-finger proteins harboring repeat epitope tags (ZF probes) for signal amplification via binding of tag-specific intracellular antibodies, or frankenbodies, fused with fluorescent proteins. We achieve this in two steps: First, we develop an anti-FLAG frankenbody that can bind FLAG-tagged proteins in diverse live-cell environments. The anti-FLAG frankenbody complements the anti-HA frankenbody, enabling two-color signal amplification from FLAG- and HA-tagged proteins. Second, we develop a pair of cell-permeable ZF probes that specifically bind two endogenous chromatin loci predicted to be involved in chromatin looping. By coupling our anti-FLAG and anti-HA frankenbodies with FLAG- and HA-tagged ZF probes, we simultaneously see the dynamics of the two loci in single living cells. This shows a close association between the two loci in the majority of cells, but the loci markedly separate from the triggered degradation of the cohesin subunit RAD21. Our ability to image two endogenous genomic loci simultaneously in single living cells provides a proof of principle that ZF probes coupled with frankenbodies are useful new tools for exploring genome dynamics in multiple colors.
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Affiliation(s)
- Yang Liu
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.,Department of Genetics, SOKENDAI, Mishima, Japan
| | - Yotaro Yamamoto
- Life Science Research Laboratories, Fujifilm Wako Pure Chemical, Amagasaki, Japan
| | - Yoshifusa Sadamura
- Life Science Research Laboratories, Fujifilm Wako Pure Chemical, Amagasaki, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
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25
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Lukacs A, Thomae AW, Krueger P, Schauer T, Venkatasubramani AV, Kochanova NY, Aftab W, Choudhury R, Forne I, Imhof A. The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila. PLoS Genet 2021; 17:e1009744. [PMID: 34424906 PMCID: PMC8412352 DOI: 10.1371/journal.pgen.1009744] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/02/2021] [Accepted: 07/27/2021] [Indexed: 12/26/2022] Open
Abstract
Postzygotic isolation by genomic conflict is a major cause for the formation of species. Despite its importance, the molecular mechanisms that result in the lethality of interspecies hybrids are still largely unclear. The genus Drosophila, which contains over 1600 different species, is one of the best characterized model systems to study these questions. We showed in the past that the expression levels of the two hybrid incompatibility factors Hmr and Lhr diverged in the two closely related Drosophila species, D. melanogaster and D. simulans, resulting in an increased level of both proteins in interspecies hybrids. The overexpression of the two proteins also leads to mitotic defects, a misregulation in the expression of transposable elements and decreased fertility in pure species. In this work, we describe a distinct six subunit protein complex containing HMR and LHR and analyse the effect of Hmr mutations on complex integrity and function. Our experiments suggest that HMR needs to bring together components of centromeric and pericentromeric chromatin to fulfil its physiological function and to cause hybrid male lethality. A major cause of biological speciation is the sterility and/or lethality of hybrids. This hybrid lethality is thought to be the consequence of two incompatible genomes of the two different species. We used the fruit fly Drosophila melanogaster as a model system to isolate a defined protein complex, which mediates this hybrid lethality. Our data suggest that this complex containing six subunits has evolved in one Drosophila species (Drosophila melanogaster) to bring together components of centromeric and pericentromeric chromatin. We show that the integrity of the complex is necessary for its genomic binding patterns and its ability to maintain fertility in female Drosophila melanogaster flies. Hybrid males between Drosophila melanogaster and the very closely related species Drosophila simulans die because they contain elevated levels of this complex. These high levels result in mitotic defects and a misregulation in the expression of transposable elements in those hybrids. Our results show that mutations that interfere with the complex’s function in Drosophila melanogaster also fail to induce lethality in hybrids suggesting that its evolutionary acquired functions in one species induce lethality in interspecies hybrids.
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Affiliation(s)
- Andrea Lukacs
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas W. Thomae
- Biomedical Center, Core Facility Bioimaging, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Peter Krueger
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tamas Schauer
- Biomedical Center, Bioinformatics Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Anuroop V. Venkatasubramani
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Natalia Y. Kochanova
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wasim Aftab
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Rupam Choudhury
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ignasi Forne
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- * E-mail:
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26
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Starkov D, Parfenyev V, Belan S. Conformational statistics of non-equilibrium polymer loops in Rouse model with active loop extrusion. J Chem Phys 2021; 154:164106. [PMID: 33940823 DOI: 10.1063/5.0048942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Motivated by the recent experimental observations of the DNA loop extrusion by protein motors, in this paper, we investigate the statistical properties of the growing polymer loops within the ideal chain model. The loop conformation is characterized statistically by the mean gyration radius and the pairwise contact probabilities. It turns out that a single dimensionless parameter, which is given by the ratio of the loop relaxation time over the time elapsed since the start of extrusion, controls the crossover between near-equilibrium and highly non-equilibrium asymptotics in the statistics of the extruded loop, regardless of the specific time dependence of the extrusion velocity. In addition, we show that two-sided and one-sided loop extruding motors produce the loops with almost identical properties. Our predictions are based on two rigorous semi-analytical methods accompanied by asymptotic analysis of slow and fast extrusion limits.
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Affiliation(s)
- Dmitry Starkov
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova av., 142432 Chernogolovka, Russia and National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
| | - Vladimir Parfenyev
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova av., 142432 Chernogolovka, Russia and National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
| | - Sergey Belan
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova av., 142432 Chernogolovka, Russia and National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
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27
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Rosin LF, Gil J, Drinnenberg IA, Lei EP. Oligopaint DNA FISH reveals telomere-based meiotic pairing dynamics in the silkworm, Bombyx mori. PLoS Genet 2021; 17:e1009700. [PMID: 34319984 PMCID: PMC8351950 DOI: 10.1371/journal.pgen.1009700] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/09/2021] [Accepted: 07/07/2021] [Indexed: 12/04/2022] Open
Abstract
Accurate chromosome segregation during meiosis is essential for reproductive success. Yet, many fundamental aspects of meiosis remain unclear, including the mechanisms regulating homolog pairing across species. This gap is partially due to our inability to visualize individual chromosomes during meiosis. Here, we employ Oligopaint FISH to investigate homolog pairing and compaction of meiotic chromosomes and resurrect a classical model system, the silkworm Bombyx mori. Our Oligopaint design combines multiplexed barcoding with secondary oligo labeling for high flexibility and low cost. These studies illustrate that Oligopaints are highly specific in whole-mount gonads and on meiotic squashes. We show that meiotic pairing is robust in both males and females and that pairing can occur through numerous partially paired intermediate structures. We also show that pairing in male meiosis occurs asynchronously and seemingly in a transcription-biased manner. Further, we reveal that meiotic bivalent formation in B. mori males is highly similar to bivalent formation in C. elegans, with both of these pathways ultimately resulting in the pairing of chromosome ends with non-paired ends facing the spindle pole. Additionally, microtubule recruitment in both C. elegans and B. mori is likely dependent on kinetochore proteins but independent of the centromere-specifying histone CENP-A. Finally, using super-resolution microscopy in the female germline, we show that homologous chromosomes remain associated at telomere domains in the absence of chiasma and after breakdown and modification to the synaptonemal complex in pachytene. These studies reveal novel insights into mechanisms of meiotic homolog pairing both with or without recombination.
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Affiliation(s)
- Leah F. Rosin
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jose Gil
- Institut Curie, PSL Research University, CNRS, Paris, France; Sorbonne Université, Institut Curie, CNRS, Paris, France
| | - Ines A. Drinnenberg
- Institut Curie, PSL Research University, CNRS, Paris, France; Sorbonne Université, Institut Curie, CNRS, Paris, France
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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28
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Li J, Lin Y, Tang Q, Li M. Understanding three-dimensional chromatin organization in diploid genomes. Comput Struct Biotechnol J 2021; 19:3589-3598. [PMID: 34257838 PMCID: PMC8246089 DOI: 10.1016/j.csbj.2021.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/17/2022] Open
Abstract
The three-dimensional (3D) organization of chromatin in the nucleus of diploid eukaryotic organisms has fascinated biologists for many years. Despite major progress in chromatin conformation studies, current knowledge regarding the spatial organization of diploid (maternal and paternal) genomes is still limited. Recent advances in Hi-C technology and data processing approaches have enabled construction of diploid Hi-C contact maps. These maps greatly accelerated the pace of novel discoveries in haplotype-resolved 3D genome studies, revealing the role of allele biased chromatin conformation in transcriptional regulation. Here, we review emerging concepts and haplotype phasing strategies of Hi-C data in 3D diploid genome studies. We discuss new insights on homologous chromosomal organization and the interplay between allelic biased chromatin architecture and several nuclear functions, explaining how haplotype-resolved Hi-C technologies have been used to resolve important biological questions.
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Affiliation(s)
- Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Lin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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29
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Child MB, Bateman JR, Jahangiri A, Reimer A, Lammers NC, Sabouni N, Villamarin D, McKenzie-Smith GC, Johnson JE, Jost D, Garcia HG. Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila. eLife 2021; 10:64412. [PMID: 34100718 PMCID: PMC8294847 DOI: 10.7554/elife.64412] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Three-dimensional eukaryotic genome organization provides the structural basis for gene regulation. In Drosophila melanogaster, genome folding is characterized by somatic homolog pairing, where homologous chromosomes are intimately paired from end to end; however, how homologs identify one another and pair has remained mysterious. Recently, this process has been proposed to be driven by specifically interacting 'buttons' encoded along chromosomes. Here, we turned this hypothesis into a quantitative biophysical model to demonstrate that a button-based mechanism can lead to chromosome-wide pairing. We tested our model using live-imaging measurements of chromosomal loci tagged with the MS2 and PP7 nascent RNA labeling systems. We show solid agreement between model predictions and experiments in the pairing dynamics of individual homologous loci. Our results strongly support a button-based mechanism of somatic homolog pairing in Drosophila and provide a theoretical framework for revealing the molecular identity and regulation of buttons.
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Affiliation(s)
- Myron Barber Child
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, United States
| | - Amir Jahangiri
- Univ Grenoble Alpes CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Armando Reimer
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Nicholas C Lammers
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Nica Sabouni
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | | | | | | | - Daniel Jost
- Univ Grenoble Alpes CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France.,Université de Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratory of Biology and Modeling of the Cell, Lyon, France
| | - Hernan G Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States
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30
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Peterson SC, Samuelson KB, Hanlon SL. Multi-Scale Organization of the Drosophila melanogaster Genome. Genes (Basel) 2021; 12:817. [PMID: 34071789 PMCID: PMC8228293 DOI: 10.3390/genes12060817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
Interphase chromatin, despite its appearance, is a highly organized framework of loops and bends. Chromosomes are folded into topologically associating domains, or TADs, and each chromosome and its homolog occupy a distinct territory within the nucleus. In Drosophila, genome organization is exceptional because homologous chromosome pairing is in both germline and somatic tissues, which promote interhomolog interactions such as transvection that can affect gene expression in trans. In this review, we focus on what is known about genome organization in Drosophila and discuss it from TADs to territory. We start by examining intrachromosomal organization at the sub-chromosome level into TADs, followed by a comprehensive analysis of the known proteins that play a key role in TAD formation and boundary establishment. We then zoom out to examine interhomolog interactions such as pairing and transvection that are abundant in Drosophila but rare in other model systems. Finally, we discuss chromosome territories that form within the nucleus, resulting in a complete picture of the multi-scale organization of the Drosophila genome.
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Affiliation(s)
| | | | - Stacey L. Hanlon
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (S.C.P.); (K.B.S.)
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31
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Li Z, Marcel N, Devkota S, Auradkar A, Hedrick SM, Gantz VM, Bier E. CopyCatchers are versatile active genetic elements that detect and quantify inter-homolog somatic gene conversion. Nat Commun 2021; 12:2625. [PMID: 33976171 PMCID: PMC8113449 DOI: 10.1038/s41467-021-22927-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/01/2021] [Indexed: 11/08/2022] Open
Abstract
CRISPR-based active genetic elements, or gene-drives, copied via homology-directed repair (HDR) in the germline, are transmitted to progeny at super-Mendelian frequencies. Active genetic elements also can generate widespread somatic mutations, but the genetic basis for such phenotypes remains uncertain. It is generally assumed that such somatic mutations are generated by non-homologous end-joining (NHEJ), the predominant double stranded break repair pathway active in somatic cells. Here, we develop CopyCatcher systems in Drosophila to detect and quantify somatic gene conversion (SGC) events. CopyCatchers inserted into two independent genetic loci reveal unexpectedly high rates of SGC in the Drosophila eye and thoracic epidermis. Focused RNAi-based genetic screens identify several unanticipated loci altering SGC efficiency, one of which (c-MYC), when downregulated, promotes SGC mediated by both plasmid and homologous chromosome-templates in human HEK293T cells. Collectively, these studies suggest that CopyCatchers can serve as effective discovery platforms to inform potential gene therapy strategies.
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Affiliation(s)
- Zhiqian Li
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Nimi Marcel
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Stephen M Hedrick
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA, USA.
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32
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Johnstone CP, Wang NB, Sevier SA, Galloway KE. Understanding and Engineering Chromatin as a Dynamical System across Length and Timescales. Cell Syst 2020; 11:424-448. [PMID: 33212016 DOI: 10.1016/j.cels.2020.09.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 12/20/2022]
Abstract
Connecting the molecular structure and function of chromatin across length and timescales remains a grand challenge to understanding and engineering cellular behaviors. Across five orders of magnitude, dynamic processes constantly reshape chromatin structures, driving spaciotemporal patterns of gene expression and cell fate. Through the interplay of structure and function, the genome operates as a highly dynamic feedback control system. Recent experimental techniques have provided increasingly detailed data that revise and augment the relatively static, hierarchical view of genomic architecture with an understanding of how dynamic processes drive organization. Here, we review how novel technologies from sequencing, imaging, and synthetic biology refine our understanding of chromatin structure and function and enable chromatin engineering. Finally, we discuss opportunities to use these tools to enhance understanding of the dynamic interrelationship of chromatin structure and function.
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Affiliation(s)
| | - Nathan B Wang
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA
| | - Stuart A Sevier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Kate E Galloway
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA.
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33
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Palladino J, Chavan A, Sposato A, Mason TD, Mellone BG. Targeted De Novo Centromere Formation in Drosophila Reveals Plasticity and Maintenance Potential of CENP-A Chromatin. Dev Cell 2020; 52:379-394.e7. [PMID: 32049040 DOI: 10.1016/j.devcel.2020.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/17/2019] [Accepted: 01/06/2020] [Indexed: 11/25/2022]
Abstract
Centromeres are essential for accurate chromosome segregation and are marked by centromere protein A (CENP-A) nucleosomes. Mis-targeted CENP-A chromatin has been shown to seed centromeres at non-centromeric DNA. However, the requirements for such de novo centromere formation and transmission in vivo remain unknown. Here, we employ Drosophila melanogaster and the LacI/lacO system to investigate the ability of targeted de novo centromeres to assemble and be inherited through development. De novo centromeres form efficiently at six distinct genomic locations, which include actively transcribed chromatin and heterochromatin, and cause widespread chromosomal instability. During tethering, de novo centromeres sometimes prevail, causing the loss of the endogenous centromere via DNA breaks and HP1-dependent epigenetic inactivation. Transient induction of de novo centromeres and chromosome healing in early embryogenesis show that, once established, these centromeres can be maintained through development. Our results underpin the ability of CENP-A chromatin to establish and sustain mitotic centromere function in Drosophila.
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Affiliation(s)
- Jason Palladino
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Ankita Chavan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Anthony Sposato
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Timothy D Mason
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Barbara G Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
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34
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Sakamoto T, Sugiyama T, Yamashita T, Matsunaga S. Plant condensin II is required for the correct spatial relationship between centromeres and rDNA arrays. Nucleus 2020; 10:116-125. [PMID: 31092096 PMCID: PMC6527393 DOI: 10.1080/19491034.2019.1616507] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Plants possess the structural maintenance of chromosome (SMC) protein complexes cohesin, condensin, and SMC5/6, which function in fundamental biological processes such as sister chromatid cohesion, chromosome condensation and segregation, and damaged DNA repair. Recently, increasing evidence in several organisms has suggested that condensin is involved in chromatin organizations during interphase. In Arabidopsis thaliana, condensin II is localized in the nucleus throughout interphase and is suggested to be required for keeping centromeres apart and the assembly of euchromatic chromosome arms. However, it remains unclear how condensin II organizes chromatin associations. Here, we first showed the high possibility that the function of condensin II as a complex is required for the disassociation of centromeres. Analysis of the rDNA array distribution revealed that condensin II is also indispensable for the association of centromeres with rDNA arrays. Reduced axial compaction of chromosomes and impaired genome integrity in condensin II mutants are not related to the disruption of chromatin organization. In contrast, the axial compaction of chromosomes by condensin II produces the force leading to the disassociation of heterologous centromeres in Drosophila melanogaster. Taken together, our data imply that the condensin II function in chromatin organization differs among eukaryotes.
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Affiliation(s)
- Takuya Sakamoto
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Tomoya Sugiyama
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Tomoe Yamashita
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Sachihiro Matsunaga
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
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35
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Boettiger A, Murphy S. Advances in Chromatin Imaging at Kilobase-Scale Resolution. Trends Genet 2020; 36:273-287. [PMID: 32007290 PMCID: PMC7197267 DOI: 10.1016/j.tig.2019.12.010] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2022]
Abstract
It is now widely appreciated that the spatial organization of the genome is nonrandom, and its complex 3D folding has important consequences for many genome processes. Recent developments in multiplexed, super-resolution microscopy have enabled an unprecedented view of the polymeric structure of chromatin - from the loose folds of whole chromosomes to the detailed loops of cis-regulatory elements that regulate gene expression. Facilitated by the use of robotics, microfluidics, and improved approaches to super-resolution, thousands to hundreds of thousands of individual cells can now be analyzed in an individual experiment. This has led to new insights into the nature of genomic structural features identified by sequencing, such as topologically associated domains (TADs), and the nature of enhancer-promoter interactions underlying transcriptional regulation. We review these recent improvements.
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Affiliation(s)
- Alistair Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
| | - Sedona Murphy
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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36
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Synaptonemal Complex-Deficient Drosophila melanogaster Females Exhibit Rare DSB Repair Events, Recurrent Copy-Number Variation, and an Increased Rate of de Novo Transposable Element Movement. G3-GENES GENOMES GENETICS 2020; 10:525-537. [PMID: 31882405 PMCID: PMC7003089 DOI: 10.1534/g3.119.400853] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Genetic stability depends on the maintenance of a variety of chromosome structures and the precise repair of DNA breaks. During meiosis, programmed double-strand breaks (DSBs) made in prophase I are normally repaired as gene conversions or crossovers. DSBs can also be made by other mechanisms, such as the movement of transposable elements (TEs), which must also be resolved. Incorrect repair of these DNA lesions can lead to mutations, copy-number changes, translocations, and/or aneuploid gametes. In Drosophila melanogaster, as in most organisms, meiotic DSB repair occurs in the presence of a rapidly evolving multiprotein structure called the synaptonemal complex (SC). Here, whole-genome sequencing is used to investigate the fate of meiotic DSBs in D. melanogaster mutant females lacking functional SC, to assay for de novo CNV formation, and to examine the role of the SC in transposable element movement in flies. The data indicate that, in the absence of SC, copy-number variation still occurs and meiotic DSB repair by gene conversion occurs infrequently. Remarkably, an 856-kilobase de novo CNV was observed in two unrelated individuals of different genetic backgrounds and was identical to a CNV recovered in a previous wild-type study, suggesting that recurrent formation of large CNVs occurs in Drosophila. In addition, the rate of novel TE insertion was markedly higher than wild type in one of two SC mutants tested, suggesting that SC proteins may contribute to the regulation of TE movement and insertion in the genome. Overall, this study provides novel insight into the role that the SC plays in genome stability and provides clues as to why the sequence, but not structure, of SC proteins is rapidly evolving.
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37
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King TD, Leonard CJ, Cooper JC, Nguyen S, Joyce EF, Phadnis N. Recurrent Losses and Rapid Evolution of the Condensin II Complex in Insects. Mol Biol Evol 2020; 36:2195-2204. [PMID: 31270536 PMCID: PMC6759200 DOI: 10.1093/molbev/msz140] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Condensins play a crucial role in the organization of genetic material by compacting and disentangling chromosomes. Based on studies in a few model organisms, the condensins I and II complexes are considered to have distinct functions, with the condensin II complex playing a role in meiosis and somatic pairing of homologous chromosomes in Drosophila. Intriguingly, the Cap-G2 subunit of condensin II is absent in Drosophila melanogaster, and this loss may be related to the high levels of chromosome pairing seen in flies. Here, we find that all three non-SMC subunits of condensin II (Cap-G2, Cap-D3, and Cap-H2) have been repeatedly and independently lost in taxa representing multiple insect orders, with some taxa lacking all three. We also find that all non-Dipteran insects display near-uniform low-pairing levels regardless of their condensin II complex composition, suggesting that some key aspects of genome organization are robust to condensin II subunit losses. Finally, we observe consistent signatures of positive selection in condensin subunits across flies and mammals. These findings suggest that these ancient complexes are far more evolutionarily labile than previously suspected, and are at the crossroads of several forms of genomic conflicts. Our results raise fundamental questions about the specific functions of the two condensin complexes in taxa that have experienced subunit losses, and open the door to further investigations to elucidate the diversity of molecular mechanisms that underlie genome organization across various life forms.
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Affiliation(s)
- Thomas D King
- School of Biological Sciences, University of Utah, Salt Lake City, UT
| | | | - Jacob C Cooper
- School of Biological Sciences, University of Utah, Salt Lake City, UT
| | - Son Nguyen
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Eric F Joyce
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Nitin Phadnis
- School of Biological Sciences, University of Utah, Salt Lake City, UT
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King TD, Johnson JE, Bateman JR. Position Effects Influence Transvection in Drosophila melanogaster. Genetics 2019; 213:1289-1299. [PMID: 31611231 PMCID: PMC6893391 DOI: 10.1534/genetics.119.302583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/03/2019] [Indexed: 01/14/2023] Open
Abstract
Transvection is an epigenetic phenomenon wherein regulatory elements communicate between different chromosomes in trans, and is thereby dependent upon the three-dimensional organization of the genome. Transvection is best understood in Drosophila, where homologous chromosomes are closely paired in most somatic nuclei, although similar phenomena have been observed in other species. Previous data have supported that the Drosophila genome is generally permissive to enhancer action in trans, a form of transvection where an enhancer on one homolog activates gene expression from a promoter on a paired homolog. However, the capacity of different genomic positions to influence the quantitative output of transvection has yet to be addressed. To investigate this question, we employed a transgenic system that assesses and compares enhancer action in cis and in trans at defined chromosomal locations. Using the strong synthetic eye-specific enhancer GMR, we show that loci supporting strong cis-expression tend to support robust enhancer action in trans, whereas locations with weaker cis-expression show reduced transvection in a fluorescent reporter assay. Our subsequent analysis is consistent with a model wherein the chromatin state of the transgenic insertion site is a primary determinant of the degree to which enhancer action in trans will be supported, whereas other factors such as locus-specific variation in somatic homolog pairing are of less importance in influencing position effects on transvection.
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Affiliation(s)
- Thomas D King
- Biology Department, Bowdoin College, Brunswick, Maine 04011
| | | | - Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, Maine 04011
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Deutschman E, Ward JR, Kumar A, Ray G, Welch N, Lemieux ME, Dasarathy S, Longworth MS. Condensin II protein dysfunction impacts mitochondrial respiration and mitochondrial oxidative stress responses. J Cell Sci 2019; 132:jcs233783. [PMID: 31653782 PMCID: PMC6899004 DOI: 10.1242/jcs.233783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/21/2019] [Indexed: 12/28/2022] Open
Abstract
The maintenance of mitochondrial respiratory function and homeostasis is essential to human health. Here, we identify condensin II subunits as novel regulators of mitochondrial respiration and mitochondrial stress responses. Condensin II is present in the nucleus and cytoplasm. While the effects of condensin II depletion on nuclear genome organization are well studied, the effects on essential cytoplasmic and metabolic processes are not as well understood. Excitingly, we observe that condensin II chromosome-associated protein (CAP) subunits individually localize to different regions of mitochondria, suggesting possible mitochondrial-specific functions independent from those mediated by the canonical condensin II holocomplex. Changes in cellular ATP levels and mitochondrial respiration are observed in condensin II CAP subunit-deficient cells. Surprisingly, we find that loss of NCAPD3 also sensitizes cells to oxidative stress. Together, these studies identify new, and possibly independent, roles for condensin II CAP subunits in preventing mitochondrial damage and dysfunction. These findings reveal a new area of condensin protein research that could contribute to the identification of targets to treat diseases where aberrant function of condensin II proteins is implicated.
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Affiliation(s)
- Emily Deutschman
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University Cleveland, OH 44106, USA
| | - Jacqueline R Ward
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Avinash Kumar
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Greeshma Ray
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Nicole Welch
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | | | - Srinivisan Dasarathy
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Michelle S Longworth
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
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40
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Mazur AK, Nguyen TS, Gladyshev E. Direct Homologous dsDNA-dsDNA Pairing: How, Where, and Why? J Mol Biol 2019; 432:737-744. [PMID: 31726060 DOI: 10.1016/j.jmb.2019.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/22/2019] [Accepted: 11/05/2019] [Indexed: 10/25/2022]
Abstract
The ability of homologous chromosomes (or selected chromosomal loci) to pair specifically in the apparent absence of DNA breakage and recombination represents a prominent feature of eukaryotic biology. The mechanism of homology recognition at the basis of such recombination-independent pairing has remained elusive. A number of studies have supported the idea that sequence homology can be sensed between intact DNA double helices in vivo. In particular, recent analyses of the two silencing phenomena in fungi, known as "repeat-induced point mutation" (RIP) and "meiotic silencing by unpaired DNA" (MSUD), have provided genetic evidence for the existence of the direct homologous dsDNA-dsDNA pairing. Both RIP and MSUD likely rely on the same search strategy, by which dsDNA segments are matched as arrays of interspersed base-pair triplets. This process is general and very efficient, yet it proceeds normally without the RecA/Rad51/Dmc1 proteins. Further studies of RIP and MSUD may yield surprising insights into the function of DNA in the cell.
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Affiliation(s)
- Alexey K Mazur
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, F-75005 Paris, France; Group Fungal Epigenomics, Department of Mycology, Institut Pasteur, Paris 75015, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Tinh-Suong Nguyen
- Group Fungal Epigenomics, Department of Mycology, Institut Pasteur, Paris 75015, France
| | - Eugene Gladyshev
- Group Fungal Epigenomics, Department of Mycology, Institut Pasteur, Paris 75015, France.
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AlHaj Abed J, Erceg J, Goloborodko A, Nguyen SC, McCole RB, Saylor W, Fudenberg G, Lajoie BR, Dekker J, Mirny LA, Wu CT. Highly structured homolog pairing reflects functional organization of the Drosophila genome. Nat Commun 2019; 10:4485. [PMID: 31582763 PMCID: PMC6776532 DOI: 10.1038/s41467-019-12208-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 08/27/2019] [Indexed: 01/14/2023] Open
Abstract
Trans-homolog interactions have been studied extensively in Drosophila, where homologs are paired in somatic cells and transvection is prevalent. Nevertheless, the detailed structure of pairing and its functional impact have not been thoroughly investigated. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, showing that homologs pair with varying precision genome-wide, in addition to establishing trans-homolog domains and compartments. We also elucidate the structure of pairing with unprecedented detail, observing significant variation across the genome and revealing at least two forms of pairing: tight pairing, spanning contiguous small domains, and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional implication genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show that disruption of pairing-promoting factors results in global changes in pairing, including the disruption of some interaction peaks.
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Affiliation(s)
- Jumana AlHaj Abed
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Anton Goloborodko
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Son C Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA
| | - Ruth B McCole
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Wren Saylor
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
- Gladstone Institutes of Data Science and Biotechnology, San Francisco, CA, 94158, USA
| | - Bryan R Lajoie
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605-0103, USA
- Illumina, San Diego, CA, USA
| | - Job Dekker
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605-0103, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
| | - C-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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42
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Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT. The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nat Commun 2019; 10:4486. [PMID: 31582744 PMCID: PMC6776651 DOI: 10.1038/s41467-019-12211-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022] Open
Abstract
Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.
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Affiliation(s)
- Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jumana AlHaj Abed
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Anton Goloborodko
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Bryan R Lajoie
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605-0103, USA
- Illumina, San Diego, CA, USA
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
- Gladstone Institutes of Data Science and Biotechnology, San Francisco, CA, 94158, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Maxim Imakaev
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Ruth B McCole
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Son C Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA
| | - Wren Saylor
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eric F Joyce
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA
| | - T Niroshini Senaratne
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Mohammed A Hannan
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Guy Nir
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Job Dekker
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605-0103, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
| | - C-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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43
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Anselm E, Thomae AW, Jeyaprakash AA, Heun P. Oligomerization of Drosophila Nucleoplasmin-Like Protein is required for its centromere localization. Nucleic Acids Res 2019; 46:11274-11286. [PMID: 30357352 PMCID: PMC6277087 DOI: 10.1093/nar/gky988] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/18/2018] [Indexed: 01/10/2023] Open
Abstract
The evolutionarily conserved nucleoplasmin family of histone chaperones has two paralogues in Drosophila, named Nucleoplasmin-Like Protein (NLP) and Nucleophosmin (NPH). NLP localizes to the centromere, yet molecular underpinnings of this localization are unknown. Moreover, similar to homologues in other organisms, NLP forms a pentamer in vitro, but the biological significance of its oligomerization has not been explored. Here, we characterize the oligomers formed by NLP and NPH in vivo and find that oligomerization of NLP is required for its localization at the centromere. We can further show that oligomerization-deficient NLP is unable to bind the centromeric protein Hybrid Male Rescue (HMR), which in turn is required for targeting the NLP oligomer to the centromere. Finally, using super-resolution microscopy we find that NLP and HMR largely co-localize in domains that are immediately adjacent to, yet distinct from centromere domains defined by the centromeric histone dCENP-A.
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Affiliation(s)
- Eduard Anselm
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Wellcome Trust Centre for Cell Biology, Edinburgh, UK
| | - Andreas W Thomae
- Biomedical Center, Core Facility Bioimaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | - Patrick Heun
- Wellcome Trust Centre for Cell Biology, Edinburgh, UK
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44
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Piwko P, Vitsaki I, Livadaras I, Delidakis C. The Role of Insulators in Transgene Transvection in Drosophila. Genetics 2019; 212:489-508. [PMID: 30948430 PMCID: PMC6553826 DOI: 10.1534/genetics.119.302165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/02/2019] [Indexed: 12/19/2022] Open
Abstract
Transvection is the phenomenon where a transcriptional enhancer activates a promoter located on the homologous chromosome. It has been amply documented in Drosophila where homologs are closely paired in most, if not all, somatic nuclei, but it has been known to rarely occur in mammals as well. We have taken advantage of site-directed transgenesis to insert reporter constructs into the same genetic locus in Drosophila and have evaluated their ability to engage in transvection by testing many heterozygous combinations. We find that transvection requires the presence of an insulator element on both homologs. Homotypic trans-interactions between four different insulators can support transvection: the gypsy insulator (GI), Wari, Fab-8 and 1A2; GI and Fab-8 are more effective than Wari or 1A2 We show that, in the presence of insulators, transvection displays the characteristics that have been previously described: it requires homolog pairing, but can happen at any of several loci in the genome; a solitary enhancer confronted with an enhancerless reporter is sufficient to drive transcription; it is weaker than the action of the same enhancer-promoter pair in cis, and it is further suppressed by cis-promoter competition. Though necessary, the presence of homotypic insulators is not sufficient for transvection; their position, number and orientation matters. A single GI adjacent to both enhancer and promoter is the optimal configuration. The identity of enhancers and promoters in the vicinity of a trans-interacting insulator pair is also important, indicative of complex insulator-enhancer-promoter interactions.
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Affiliation(s)
- Pawel Piwko
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion 70013, Crete, Greece
- Department of Biology, University of Crete, Heraklion 70013, Crete, Greece
| | - Ilektra Vitsaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion 70013, Crete, Greece
- Department of Biology, University of Crete, Heraklion 70013, Crete, Greece
| | - Ioannis Livadaras
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion 70013, Crete, Greece
| | - Christos Delidakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion 70013, Crete, Greece
- Department of Biology, University of Crete, Heraklion 70013, Crete, Greece
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45
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Kim S, Dunham MJ, Shendure J. A combination of transcription factors mediates inducible interchromosomal contacts. eLife 2019; 8:e42499. [PMID: 31081754 PMCID: PMC6548505 DOI: 10.7554/elife.42499] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 05/11/2019] [Indexed: 12/30/2022] Open
Abstract
The genome forms specific three-dimensional contacts in response to cellular or environmental conditions. However, it remains largely unknown which proteins specify and mediate such contacts. Here we describe an assay, MAP-C (Mutation Analysis in Pools by Chromosome conformation capture), that simultaneously characterizes the effects of hundreds of cis or trans-acting mutations on a chromosomal contact. Using MAP-C, we show that inducible interchromosomal pairing between HAS1pr-TDA1pr alleles in saturated cultures of Saccharomyces yeast is mediated by three transcription factors, Leu3, Sdd4 (Ypr022c), and Rgt1. The coincident, combined binding of all three factors is strongest at the HAS1pr-TDA1pr locus and is also specific to saturated conditions. We applied MAP-C to further explore the biochemical mechanism of these contacts, and find they require the structured regulatory domain of Rgt1, but no known interaction partners of Rgt1. Altogether, our results demonstrate MAP-C as a powerful method for dissecting the mechanistic basis of chromosome conformation.
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Affiliation(s)
- Seungsoo Kim
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - Maitreya J Dunham
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - Jay Shendure
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Howard Hughes Medical InstituteSeattleUnited States
- Brotman Baty Institute for Precision MedicineSeattleUnited States
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46
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Tian K, Henderson RE, Parker R, Brown A, Johnson JE, Bateman JR. Two modes of transvection at the eyes absent gene of Drosophila demonstrate plasticity in transcriptional regulatory interactions in cis and in trans. PLoS Genet 2019; 15:e1008152. [PMID: 31075100 PMCID: PMC6530868 DOI: 10.1371/journal.pgen.1008152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/22/2019] [Accepted: 04/23/2019] [Indexed: 01/10/2023] Open
Abstract
For many genes, proper gene expression requires coordinated and dynamic interactions between multiple regulatory elements, each of which can either promote or silence transcription. In Drosophila, the complexity of the regulatory landscape is further complicated by the tight physical pairing of homologous chromosomes, which can permit regulatory elements to interact in trans, a phenomenon known as transvection. To better understand how gene expression can be programmed through cis- and trans-regulatory interactions, we analyzed transvection effects for a collection of alleles of the eyes absent (eya) gene. We find that trans-activation of a promoter by the eya eye-specific enhancers is broadly supported in many allelic backgrounds, and that the availability of an enhancer to act in trans can be predicted based on the molecular lesion of an eya allele. Furthermore, by manipulating promoter availability in cis and in trans, we demonstrate that the eye-specific enhancers of eya show plasticity in their promoter preference between two different transcriptional start sites, which depends on promoter competition between the two potential targets. Finally, we show that certain alleles of eya demonstrate pairing-sensitive silencing resulting from trans-interactions between Polycomb Response Elements (PREs), and genetic and genomic data support a general role for PcG proteins in mediating transcriptional silencing at eya. Overall, our data highlight how eya gene regulation relies upon a complex but plastic interplay between multiple enhancers, promoters, and PREs. Gene regulation requires interactions between regions of DNA known as regulatory elements, which, in combination, determine where and when a gene will be active or silenced. Some genes use just a few regulatory elements, whereas others rely on highly complex interactions between many different elements that are poorly understood. While we typically imagine regulatory elements interacting with one another along the length of a single chromosome, in a curious phenomenon called transvection, elements can communicate between two different chromosomes that are held in close proximity. Here, we use the study of transvection to better understand how different regulatory elements contribute to the expression of eyes absent (eya), a gene required for proper eye development in Drosophila. Our data show that a class of elements that initiate eya gene expression, called promoters, will compete with one another for activation by eya’s enhancers, a second class of regulatory element, with the promoter that is closest to the enhancers being the favored target for activation. Furthermore, our study of transvection uncovers an important role for a silencing element, called a PRE, in opposing eya gene expression. Overall, our study sheds new light on how different elements combine to produce patterned expression of eya.
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Affiliation(s)
- Katherine Tian
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Rachel E. Henderson
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Reyna Parker
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Alexia Brown
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Justine E. Johnson
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Jack R. Bateman
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
- * E-mail:
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47
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Wallace HA, Rana V, Nguyen HQ, Bosco G. Condensin II subunit NCAPH2 associates with shelterin protein TRF1 and is required for telomere stability. J Cell Physiol 2019; 234:20755-20768. [PMID: 31026066 PMCID: PMC6767372 DOI: 10.1002/jcp.28681] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 03/19/2019] [Indexed: 12/24/2022]
Abstract
Condensin II subunits are known to be expressed and localized to interphase nuclei of eukaryotic cells. Although some studies have shown that condensin II likely exerts axial compaction forces, organizes chromosome territories, and has possible transcriptional modulatory functions, the full range of condensin II interphase activities are not known. In particular, it is not known if condensin II interphase activities are generally genome‐wide or if they have additional local activities unique to specific chromosomal structures such as telomeres. Here, we find that NCAPH2 interacts with TRF1 and these two proteins co‐localize at telomeres. Depletion of NCAPH2 leads to ATR‐dependent accumulation of 53BP1 and γH2AX DNA damage foci, including damage specific to telomeres. Furthermore, depletion of NCAPH2 results in a fragile telomere phenotype and apparent sister‐telomere fusions only days after NCAPH2 depletion. Taken together these observations suggest that NCAPH2 promotes telomere stability, possibly through a direct interaction with the TRF1 shelterin component, and prevents telomere dysfunction resulting from impaired DNA replication. Because proper telomere function is essential for chromosome integrity these observations reveal a previously unappreciated function for NCAPH2 in ensuring genome and telomere stability.
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Affiliation(s)
| | - Vibhuti Rana
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Huy Q Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Giovanni Bosco
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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48
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Cardozo Gizzi AM, Cattoni DI, Fiche JB, Espinola SM, Gurgo J, Messina O, Houbron C, Ogiyama Y, Papadopoulos GL, Cavalli G, Lagha M, Nollmann M. Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms. Mol Cell 2019; 74:212-222.e5. [DOI: 10.1016/j.molcel.2019.01.011] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/27/2018] [Accepted: 01/08/2019] [Indexed: 01/30/2023]
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Rowley MJ, Lyu X, Rana V, Ando-Kuri M, Karns R, Bosco G, Corces VG. Condensin II Counteracts Cohesin and RNA Polymerase II in the Establishment of 3D Chromatin Organization. Cell Rep 2019; 26:2890-2903.e3. [PMID: 30865881 PMCID: PMC6424357 DOI: 10.1016/j.celrep.2019.01.116] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/02/2019] [Accepted: 01/30/2019] [Indexed: 12/22/2022] Open
Abstract
Interaction domains in Drosophila chromosomes form by segregation of active and inactive chromatin in the absence of CTCF loops, but the role of transcription versus other architectural proteins in chromatin organization is unclear. Here, we find that positioning of RNAPII via transcription elongation is essential in the formation of gene loops, which in turn interact to form compartmental domains. Inhibition of transcription elongation or depletion of cohesin decreases gene looping and formation of active compartmental domains. In contrast, depletion of condensin II, which also localizes to active chromatin, causes increased gene looping, formation of compartmental domains, and stronger intra-chromosomal compartmental interactions. Condensin II has a similar role in maintaining inter-chromosomal interactions responsible for pairing between homologous chromosomes, whereas inhibition of transcription elongation or cohesin depletion has little effect on homolog pairing. The results suggest distinct roles for cohesin and condensin II in the establishment of 3D nuclear organization in Drosophila.
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Affiliation(s)
- M Jordan Rowley
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Xiaowen Lyu
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Vibhuti Rana
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Masami Ando-Kuri
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Rachael Karns
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Giovanni Bosco
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA.
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Mitotic antipairing of homologous and sex chromosomes via spatial restriction of two haploid sets. Proc Natl Acad Sci U S A 2018; 115:E12235-E12244. [PMID: 30530674 PMCID: PMC6310853 DOI: 10.1073/pnas.1809583115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitotic recombination must be prevented to maintain genetic stability across daughter cells, but the underlying mechanism remains elusive. We report that mammalian cells impede homologous chromosome pairing during mitosis by keeping the two haploid chromosome sets apart, positioning them to either side of a meridional plane defined by the centrosomes. Chromosome oscillation analysis revealed collective genome behavior of noninteracting chromosome sets. Male translocation mice with a maternal-derived supernumerary chromosome display the tracer chromosome exclusively to the haploid set containing the X chromosome. This haploid set-based antipairing motif is shared by multiple cell types, is doubled in tetraploid cells, and is lost in carcinoma cells. The data provide a model of nuclear polarity through the antipairing of homologous chromosomes during mitosis. Pairing homologous chromosomes is required for recombination. However, in nonmeiotic stages it can lead to detrimental consequences, such as allelic misregulation and genome instability, and is rare in human somatic cells. How mitotic recombination is prevented—and how genetic stability is maintained across daughter cells—is a fundamental, unanswered question. Here, we report that both human and mouse cells impede homologous chromosome pairing by keeping two haploid chromosome sets apart throughout mitosis. Four-dimensional analysis of chromosomes during cell division revealed that a haploid chromosome set resides on either side of a meridional plane, crossing two centrosomes. Simultaneous tracking of chromosome oscillation and the spindle axis, using fluorescent CENP-A and centrin1, respectively, demonstrates collective genome behavior/segregation of two haploid sets throughout mitosis. Using 3D chromosome imaging of a translocation mouse with a supernumerary chromosome, we found that this maternally derived chromosome is positioned by parental origin. These data, taken together, support the identity of haploid sets by parental origin. This haploid set-based antipairing motif is shared by multiple cell types, doubles in tetraploid cells, and is lost in a carcinoma cell line. The data support a mechanism of nuclear polarity that sequesters two haploid sets along a subcellular axis. This topological segregation of haploid sets revisits an old model/paradigm and provides implications for maintaining mitotic fidelity.
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