1
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Marshall WF, Fung JC. Modeling homologous chromosome recognition via nonspecific interactions. Proc Natl Acad Sci U S A 2024; 121:e2317373121. [PMID: 38722810 PMCID: PMC11098084 DOI: 10.1073/pnas.2317373121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/18/2024] [Indexed: 05/18/2024] Open
Abstract
In many organisms, most notably Drosophila, homologous chromosomes associate in somatic cells, a phenomenon known as somatic pairing, which takes place without double strand breaks or strand invasion, thus requiring some other mechanism for homologs to recognize each other. Several studies have suggested a "specific button" model, in which a series of distinct regions in the genome, known as buttons, can associate with each other, mediated by different proteins that bind to these different regions. Here, we use computational modeling to evaluate an alternative "button barcode" model, in which there is only one type of recognition site or adhesion button, present in many copies in the genome, each of which can associate with any of the others with equal affinity. In this model, buttons are nonuniformly distributed, such that alignment of a chromosome with its correct homolog, compared with a nonhomolog, is energetically favored; since to achieve nonhomologous alignment, chromosomes would be required to mechanically deform in order to bring their buttons into mutual register. By simulating randomly generated nonuniform button distributions, many highly effective button barcodes can be easily found, some of which achieve virtually perfect pairing fidelity. This model is consistent with existing literature on the effect of translocations of different sizes on homolog pairing. We conclude that a button barcode model can attain highly specific homolog recognition, comparable to that seen in actual cells undergoing somatic homolog pairing, without the need for specific interactions. This model may have implications for how meiotic pairing is achieved.
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Affiliation(s)
- Wallace F. Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94158
| | - Jennifer C. Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA94158
- Center for Reproductive Sciences, University of California, San Francisco, CA94158
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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:e2305706. [PMID: 38582509 DOI: 10.1002/advs.202305706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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 Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Mengnan He
- Wildlife Conservation Research Department, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610057, China
| | - Hua Kui
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingyi Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ziyu Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuwei Gou
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Qianzi Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fanli Kong
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
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3
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Gutnik S, You JE, Sawh AN, Andriollo A, Mango SE. Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes. Genome Biol 2024; 25:71. [PMID: 38486337 PMCID: PMC10941459 DOI: 10.1186/s13059-024-03199-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024] Open
Abstract
Recent advances in microscopy have enabled studying chromosome organization at the single-molecule level, yet little is known about inherited chromosome organization. Here we adapt single-molecule chromosome tracing to distinguish two C. elegans strains (N2 and HI) and find that while their organization is similar, the N2 chromosome influences the folding parameters of the HI chromosome, in particular the step size, across generations. Furthermore, homologous chromosomes overlap frequently, but alignment between homologous regions is rare, suggesting that transvection is unlikely. We present a powerful tool to investigate chromosome architecture and to track the parent of origin.
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Affiliation(s)
- Silvia Gutnik
- Biozentrum, University of Basel, 4056, Basel, Switzerland
- Current address: University Children's Hospital Zürich, Pediatric Oncology and Children's Research Center, Balgrist Campus AG, Lengghalde 5, 8008, Zürich, Switzerland
| | - Jia Emil You
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Ahilya N Sawh
- Biozentrum, University of Basel, 4056, Basel, Switzerland
- Current address: Department of Biochemistry, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Aude Andriollo
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Susan E Mango
- Biozentrum, University of Basel, 4056, Basel, Switzerland.
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4
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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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5
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Marshall WF, Fung JC. Homologous chromosome recognition via nonspecific interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544427. [PMID: 37333079 PMCID: PMC10274854 DOI: 10.1101/2023.06.09.544427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
In many organisms, most notably Drosophila, homologous chromosomes in somatic cells associate with each other, a phenomenon known as somatic homolog pairing. Unlike in meiosis, where homology is read out at the level of DNA sequence complementarity, somatic homolog pairing takes place without double strand breaks or strand invasion, thus requiring some other mechanism for homologs to recognize each other. Several studies have suggested a "specific button" model, in which a series of distinct regions in the genome, known as buttons, can associate with each other, presumably mediated by different proteins that bind to these different regions. Here we consider an alternative model, which we term the "button barcode" model, in which there is only one type of recognition site or adhesion button, present in many copies in the genome, each of which can associate with any of the others with equal affinity. An important component of this model is that the buttons are non-uniformly distributed, such that alignment of a chromosome with its correct homolog, compared with a non-homolog, is energetically favored; since to achieve nonhomologous alignment, chromosomes would be required to mechanically deform in order to bring their buttons into mutual register. We investigated several types of barcodes and examined their effect on pairing fidelity. We found that high fidelity homolog recognition can be achieved by arranging chromosome pairing buttons according to an actual industrial barcode used for warehouse sorting. By simulating randomly generated non-uniform button distributions, many highly effective button barcodes can be easily found, some of which achieve virtually perfect pairing fidelity. This model is consistent with existing literature on the effect of translocations of different sizes on homolog pairing. We conclude that a button barcode model can attain highly specific homolog recognition, comparable to that seen in actual cells undergoing somatic homolog pairing, without the need for specific interactions. This model may have implications for how meiotic pairing is achieved.
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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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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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8
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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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9
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Roy S, Juste SS, Sneider M, Auradkar A, Klanseck C, Li Z, Julio AHF, Lopez del Amo V, Bier E, Guichard A. Cas9/Nickase-induced allelic conversion by homologous chromosome-templated repair in Drosophila somatic cells. SCIENCE ADVANCES 2022; 8:eabo0721. [PMID: 35776792 PMCID: PMC10883370 DOI: 10.1126/sciadv.abo0721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Repair of double-strand breaks (DSBs) in somatic cells is primarily accomplished by error-prone nonhomologous end joining and less frequently by precise homology-directed repair preferentially using the sister chromatid as a template. Here, a Drosophila system performs efficient somatic repair of both DSBs and single-strand breaks (SSBs) using intact sequences from the homologous chromosome in a process we refer to as homologous chromosome-templated repair (HTR). Unexpectedly, HTR-mediated allelic conversion at the white locus was more efficient (40 to 65%) in response to SSBs induced by Cas9-derived nickases D10A or H840A than to DSBs induced by fully active Cas9 (20 to 30%). Repair phenotypes elicited by Nickase versus Cas9 differ in both developmental timing (late versus early stages, respectively) and the production of undesired mutagenic events (rare versus frequent). Nickase-mediated HTR represents an efficient and unanticipated mechanism for allelic correction, with far-reaching potential applications in the field of gene editing.
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Affiliation(s)
- Sitara Roy
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Sara Sanz Juste
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Marketta Sneider
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Carissa Klanseck
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Zhiqian Li
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Alison Henrique Ferreira Julio
- Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Ilha do Fundão, Rio de Janeiro, 21941-902 RJ, Brazil
| | - Victor Lopez del Amo
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA 92093-0335, USA
| | - Annabel Guichard
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
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10
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Abstract
Increasing evidence indicates that non-DNA sequence-based epigenetic information can be inherited across several generations in organisms ranging from yeast to plants to humans. This raises the possibility of heritable 'epimutations' contributing to heritable phenotypic variation and thus to evolution. Recent work has shed light on both the signals that underpin these epimutations, including DNA methylation, histone modifications and non-coding RNAs, and the mechanisms by which they are transmitted across generations at the molecular level. These mechanisms can vary greatly among species and have a more limited effect in mammals than in plants and other animal species. Nevertheless, common principles are emerging, with transmission occurring either via direct replicative mechanisms or indirect reconstruction of the signal in subsequent generations. As these processes become clearer we continue to improve our understanding of the distinctive features and relative contribution of DNA sequence and epigenetic variation to heritable differences in phenotype.
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11
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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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12
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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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13
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Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Rep 2021; 35:109274. [PMID: 34161767 PMCID: PMC8317686 DOI: 10.1016/j.celrep.2021.109274] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/14/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022] Open
Abstract
Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.
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Affiliation(s)
- Ximena Contreras
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Nicole Amberg
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | | | - Andi H Hansen
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Johanna Sonntag
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Lill Andersen
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Tina Bernthaler
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Carmen Streicher
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Anna Heger
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Randy L Johnson
- Department of Biochemistry and Molecular Biology, University of Texas, Houston, TX 77030, USA
| | - Lindsay A Schwarz
- HHMI and Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Liqun Luo
- HHMI and Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Thomas Rülicke
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
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14
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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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15
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Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science 2021; 372:984-989. [PMID: 34045355 PMCID: PMC8172041 DOI: 10.1126/science.abe2218] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/16/2021] [Indexed: 01/01/2023]
Abstract
We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
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Affiliation(s)
- Claire Hoencamp
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Ahmed M O Elbatsh
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | | | - Jonne A Raaijmakers
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Tom van Schaik
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | | | - Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - SP, 15054-000, Brazil
| | - Roy G H P van Heesbeen
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Bram van den Broek
- BioImaging Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Aditya N Mhaskar
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Brian Glenn St Hilaire
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melanie Pham
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zane Colaric
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhenzhen Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
| | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Namita Mitra
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Lui
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weijie Yao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leonid L Moroz
- Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA
| | - Andrea Kohn
- Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA
| | - Judy St Leger
- Department of Biosciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
| | | | | | | | - Fabian Lim
- Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emma Farley
- Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), 06466 Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University Göttingen, 37075 Göttingen, Germany
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Alexander Haddad
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Chauss
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ayse Sena Mutlu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Evin Hildebrandt
- Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA
| | - Hans H Cheng
- Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA
| | | | - Theresa L U Burnham
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA 95616, USA
- Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA
| | - Kevin A Hovel
- Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA
| | - Andrew J Beel
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pierre-Jean Mattei
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Gregory Cary
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo CSIC, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Federica Di Palma
- Department of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Asha S Multani
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sen Pathak
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Liesl Nel-Themaat
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - René H Medema
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, TX 77005, USA
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin D Rowland
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
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16
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Galouzis CC, Prud'homme B. Transvection regulates the sex-biased expression of a fly X-linked gene. Science 2021; 371:396-400. [PMID: 33479152 DOI: 10.1126/science.abc2745] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022]
Abstract
Sexual dimorphism in animals results from sex-biased gene expression patterns. These patterns are controlled by genetic sex determination hierarchies that establish the sex of an individual. Here we show that the male-biased wing expression pattern of the Drosophila biarmipes gene yellow, located on the X chromosome, is independent of the fly sex determination hierarchy. Instead, we find that a regulatory interaction between yellow alleles on homologous chromosomes (a process known as transvection) silences the activity of a yellow enhancer functioning in the wing. Therefore, this enhancer can be active in males (XY) but not in females (XX). This transvection-dependent enhancer silencing requires the yellow intron and the chromatin architecture protein Mod(mdg4). Our results suggest that transvection can contribute more generally to the sex-biased expression of X-linked genes.
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Affiliation(s)
- Charalampos Chrysovalantis Galouzis
- Aix-Marseille Université, CNRS, Institut de Biologie du Développement de Marseille (IBDM), Campus de Luminy Case 907, 13288 Marseille Cedex 9, France
| | - Benjamin Prud'homme
- Aix-Marseille Université, CNRS, Institut de Biologie du Développement de Marseille (IBDM), Campus de Luminy Case 907, 13288 Marseille Cedex 9, France.
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17
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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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18
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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: 33] [Impact Index Per Article: 6.6] [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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19
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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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20
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Nguyen HQ, Lee SD, Wu CT. Paircounting. Trends Genet 2019; 35:787-790. [PMID: 31521404 DOI: 10.1016/j.tig.2019.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/24/2019] [Indexed: 10/26/2022]
Abstract
X inactivation presents two longstanding puzzles: the counting and choice of X chromosomes. Here, we consider counting and choice in the context of pairing, both of the X and of the autosomes.
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Affiliation(s)
- Huy Q Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - S Dean Lee
- Department of Genetics, Harvard Medical School, Boston, MA 02115, 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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21
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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: 11] [Impact Index Per Article: 2.2] [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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22
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Kizer M, Huntress ID, Walcott BD, Fraser K, Bystroff C, Wang X. Complex between a Multicrossover DNA Nanostructure, PX-DNA, and T7 Endonuclease I. Biochemistry 2019; 58:1332-1342. [PMID: 30794750 DOI: 10.1021/acs.biochem.9b00057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Paranemic crossover DNA (PX-DNA) is a four-stranded multicrossover structure that has been implicated in recombination-independent recognition of homology. Although existing evidence has suggested that PX is the DNA motif in homologous pairing (HP), this conclusion remains ambiguous. Further investigation is needed but will require development of new tools. Here, we report characterization of the complex between PX-DNA and T7 endonuclease I (T7endoI), a junction-resolving protein that could serve as the prototype of an anti-PX ligand (a critical prerequisite for the future development of such tools). Specifically, nuclease-inactive T7endoI was produced and its ability to bind to PX-DNA was analyzed using a gel retardation assay. The molar ratio of PX to T7endoI was determined using gel electrophoresis and confirmed by the Hill equation. Hydroxyl radical footprinting of T7endoI on PX-DNA is used to verify the positive interaction between PX and T7endoI and to provide insight into the binding region. Cleavage of PX-DNA by wild-type T7endoI produces DNA fragments, which were used to identify the interacting sites on PX for T7endoI and led to a computational model of their interaction. Altogether, this study has identified a stable complex of PX-DNA and T7endoI and lays the foundation for engineering an anti-PX ligand, which can potentially assist in the study of molecular mechanisms for HP at an advanced level.
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Affiliation(s)
- Megan Kizer
- Department of Chemistry and Chemical Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Ian D Huntress
- Programs of Bioinformatics and Molecular Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Benjamin D Walcott
- Department of Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Keith Fraser
- Department of Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Christopher Bystroff
- Department of Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Xing Wang
- Department of Chemistry and Chemical Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
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23
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Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet 2018; 14:e1007872. [PMID: 30586358 PMCID: PMC6324821 DOI: 10.1371/journal.pgen.1007872] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/08/2019] [Accepted: 12/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chromosome organization is crucial for genome function. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Focusing on chromosomal regions that contribute to compartments, we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Imaging through the depths of entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method-integrative modeling of genomic regions (IMGR)-to increase the genomic resolution of our traces to 10 kb.
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MESH Headings
- Cells, Cultured
- Chromosome Painting/methods
- Chromosome Structures/chemistry
- Chromosome Structures/genetics
- Chromosome Structures/ultrastructure
- Chromosome Walking/methods
- Chromosomes, Human, Pair 19/chemistry
- Chromosomes, Human, Pair 19/genetics
- Chromosomes, Human, Pair 19/ultrastructure
- Female
- Fluorescent Dyes
- Humans
- Imaging, Three-Dimensional
- In Situ Hybridization, Fluorescence/methods
- Male
- Models, Genetic
- Oligonucleotide Probes
- Pedigree
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Affiliation(s)
- Guy Nir
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Irene Farabella
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cynthia Pérez Estrada
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - Carl G. Ebeling
- Bruker Nano Inc., Salt Lake City, Utah, United States of America
| | - Brian J. Beliveau
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Hiroshi M. Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Son C. Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shyamtanu Chattoraj
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jumana AlHaj Abed
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nuno M. C. Martins
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Huy Q. Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mohammed A. Hannan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sheikh Russell
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Neva C. Durand
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
| | - Suhas S. P. Rao
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jocelyn Y. Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paula Soler-Vila
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | | | | | - Jeff A. Stuckey
- Bruker Nano Inc., Middleton, Wisconsin, United States of America
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, United States of America
| | - Marc A. Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - C.-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
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24
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Comparing and Contrasting the Effects of Drosophila Condensin II Subunit dCAP-D3 Overexpression and Depletion in Vivo. Genetics 2018; 210:531-546. [PMID: 30068527 PMCID: PMC6216582 DOI: 10.1534/genetics.118.301344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/31/2018] [Indexed: 11/18/2022] Open
Abstract
The Condensin II complex plays important, conserved roles in genome organization throughout the cell cycle and in the regulation of gene expression. Previous studies have linked decreased Condensin II subunit expression with a variety of diseases. Here, we show that elevated levels of Condensin II subunits are detected in somatic cancers. To evaluate potential biological effects of elevated Condensin II levels, we overexpressed the Condensin II subunit, dCAP-D3 in Drosophila melanogaster larval tissues and examined the effects on the mitotic- and interphase-specific functions of Condensin II. Interestingly, while ubiquitous overexpression resulted in pupal lethality, tissue specific overexpression of dCAP-D3 caused formation of nucleoplasmic protein aggregates which slowed mitotic prophase progression, mimicking results observed when dCAP-D3 levels are depleted. Surprisingly, dCAP-D3 aggregate formation resulted in faster transitions from metaphase to anaphase. Overexpressed dCAP-D3 protein failed to precipitate other Condensin II subunits in nondividing tissues, but did cause changes to gene expression which occurred in a manner opposite of what was observed when dCAP-D3 levels were depleted in both dividing and nondividing tissues. Our findings show that altering dCAP-D3 levels in either direction has detrimental effects on mitotic timing, the regulation of gene expression, and organism development. Taken together, these data suggest that the different roles for Condensin II throughout the cell cycle may be independent of each other and/or that dCAP-D3 may possess functions that are separate from those involving its association with the Condensin II complex. If conserved, these findings could have implications for tumors harboring elevated CAP-D3 levels.
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25
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Wang X, Chandrasekaran AR, Shen Z, Ohayon YP, Wang T, Kizer ME, Sha R, Mao C, Yan H, Zhang X, Liao S, Ding B, Chakraborty B, Jonoska N, Niu D, Gu H, Chao J, Gao X, Li Y, Ciengshin T, Seeman NC. Paranemic Crossover DNA: There and Back Again. Chem Rev 2018; 119:6273-6289. [PMID: 29911864 DOI: 10.1021/acs.chemrev.8b00207] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX2, has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a new role directly in basic biology, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes. This review discusses the many attributes and usages of PX-DNA-its design, characteristics, applications, and potential biological relevance-and aims to accelerate the understanding of PX-DNA motif in its many roles and manifestations.
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Affiliation(s)
- Xing Wang
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | | | - Zhiyong Shen
- College of Chemistry and Materials Science , Anhui Normal University , Wuhu , Anhui 241000 , China
| | - Yoel P Ohayon
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tong Wang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Megan E Kizer
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Ruojie Sha
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Chengde Mao
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Hao Yan
- Department of Chemistry and Biochemistry and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xiaoping Zhang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Shiping Liao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Baoquan Ding
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Banani Chakraborty
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Natasha Jonoska
- Department of Mathematics and Statistics , University of South Florida , Tampa , Florida 33620 , United States
| | - Dong Niu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Hongzhou Gu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Jie Chao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Xiang Gao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Yuhang Li
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tanashaya Ciengshin
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , New York , New York 10012 , United States
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26
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Bitran A, Chiang WY, Levine E, Prentiss M. Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA. PLoS Comput Biol 2017; 13:e1005421. [PMID: 28257444 PMCID: PMC5360337 DOI: 10.1371/journal.pcbi.1005421] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/21/2017] [Accepted: 02/21/2017] [Indexed: 12/03/2022] Open
Abstract
Self-organization in the cell relies on the rapid and specific binding of molecules to their cognate targets. Correct bindings must be stable enough to promote the desired function even in the crowded and fluctuating cellular environment. In systems with many nearly matched targets, rapid and stringent formation of stable products is challenging. Mechanisms that overcome this challenge have been previously proposed, including separating the process into multiple stages; however, how particular in vivo systems overcome the challenge remains unclear. Here we consider a kinetic system, inspired by homology dependent pairing between double stranded DNA in bacteria. By considering a simplified tractable model, we identify different homology testing stages that naturally occur in the system. In particular, we first model dsDNA molecules as short rigid rods containing periodically spaced binding sites. The interaction begins when the centers of two rods collide at a random angle. For most collision angles, the interaction energy is weak because only a few binding sites near the collision point contribute significantly to the binding energy. We show that most incorrect pairings are rapidly rejected at this stage. In rare cases, the two rods enter a second stage by rotating into parallel alignment. While rotation increases the stability of matched and nearly matched pairings, subsequent rotational fluctuations reduce kinetic trapping. Finally, in vivo chromosome are much longer than the persistence length of dsDNA, so we extended the model to include multiple parallel collisions between long dsDNA molecules, and find that those additional interactions can greatly accelerate the searching. Protein folding and the binding of sequence dependent proteins to DNA are examples of self-assembling systems in which the binding energy varies continuously throughout the interaction. Previous theoretical work has highlighted the importance of dividing the interaction into separate stages characterized by interaction times and binding energies that vary by orders of magnitude. Insight into how such a division might naturally arise and promote accurate and efficient self-assembly is provided by our study of a simple tractable model inspired by the homology dependent pairing of double stranded DNA molecules in vivo. In the model, the binding energy is controlled by one single continuously tunable variable whose natural evolution creates stages that efficiently and accurately form stable products.
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Affiliation(s)
- Amir Bitran
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Wei-Yin Chiang
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Erel Levine
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
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27
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Gladyshev E, Kleckner N. Recombination-independent recognition of DNA homology for repeat-induced point mutation. Curr Genet 2016; 63:389-400. [PMID: 27628707 DOI: 10.1007/s00294-016-0649-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/04/2016] [Accepted: 09/06/2016] [Indexed: 12/31/2022]
Abstract
Numerous cytogenetic observations have shown that homologous chromosomes (or individual chromosomal loci) can engage in specific pairing interactions in the apparent absence of DNA breakage and recombination, suggesting that canonical recombination-mediated mechanisms may not be the only option for sensing DNA/DNA homology. One proposed mechanism for such recombination-independent homology recognition involves direct contacts between intact double-stranded DNA molecules. The strongest in vivo evidence for the existence of such a mechanism is provided by the phenomena of homology-directed DNA modifications in fungi, known as repeat-induced point mutation (RIP, discovered in Neurospora crassa) and methylation-induced premeiotically (MIP, discovered in Ascobolus immersus). In principle, Neurospora RIP can detect the presence of gene-sized DNA duplications irrespectively of their origin, underlying nucleotide sequence, coding capacity or relative, as well as absolute positions in the genome. Once detected, both sequence copies are altered by numerous cytosine-to-thymine (C-to-T) mutations that extend specifically over the duplicated region. We have recently shown that Neurospora RIP does not require MEI-3, the only RecA/Rad51 protein in this organism, consistent with a recombination-independent mechanism. Using an ultra-sensitive assay for RIP mutation, we have defined additional features of this process. We have shown that RIP can detect short islands of homology of only three base-pairs as long as many such islands are arrayed with a periodicity of 11 or 12 base-pairs along a pair of DNA molecules. While the presence of perfect homology is advantageous, it is not required: chromosomal segments with overall sequence identity of only 35-36 % can still be recognized by RIP. Importantly, in order for this process to work efficiently, participating DNA molecules must be able to co-align along their lengths. Based on these findings, we have proposed a model, in which sequence homology is detected by direct interactions between slightly-extended double-stranded DNAs. As a next step, it will be important to determine if the uncovered principles also apply to other processes that involve recombination-independent interactions between homologous chromosomal loci in vivo as well as to protein-free DNA/DNA interactions that were recently observed under biologically relevant conditions in vitro.
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Affiliation(s)
- Eugene Gladyshev
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Room NW140, Cambridge, MA, 02138, USA.
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Room NW140, Cambridge, MA, 02138, USA.
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28
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Joyce EF, Erceg J, Wu CT. Pairing and anti-pairing: a balancing act in the diploid genome. Curr Opin Genet Dev 2016; 37:119-128. [PMID: 27065367 DOI: 10.1016/j.gde.2016.03.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/02/2016] [Accepted: 03/05/2016] [Indexed: 12/22/2022]
Abstract
The presence of maternal and paternal homologs appears to be much more than just a doubling of genetic material. We know this because genomes have evolved elaborate mechanisms that permit homologous regions to sense and then respond to each other. One way in which homologs communicate is to come into contact and, in fact, Dipteran insects such as Drosophila excel at this task, aligning all pairs of maternal and paternal chromosomes, end-to-end, in essentially all somatic tissues throughout development. Here, we reexamine the widely held tenet that extensive somatic pairing of homologous sequences cannot occur in mammals and suggest, instead, that pairing may be a widespread and significant potential that has gone unnoticed in mammals because they expend considerable effort to prevent it. We then extend this discussion to interchromosomal interactions, in general, and speculate about the potential of nuclear organization and pairing to impact inheritance.
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Affiliation(s)
- Eric F Joyce
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - C-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
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29
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Fujioka M, Mistry H, Schedl P, Jaynes JB. Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans. PLoS Genet 2016; 12:e1005889. [PMID: 26910731 PMCID: PMC4765946 DOI: 10.1371/journal.pgen.1005889] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/30/2016] [Indexed: 12/11/2022] Open
Abstract
The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible both for subdividing the chromatin into discrete domains and for determining the topological organization of these domains. Central to the architectural functions of insulators are homologous and heterologous insulator:insulator pairing interactions. The former (pairing between copies of the same insulator) dictates the process of homolog alignment and pairing in trans, while the latter (pairing between different insulators) defines the topology of looped domains in cis. To elucidate the principles governing these architectural functions, we use two insulators, Homie and Nhomie, that flank the Drosophila even skipped locus. We show that homologous insulator interactions in trans, between Homie on one homolog and Homie on the other, or between Nhomie on one homolog and Nhomie on the other, mediate transvection. Critically, these homologous insulator:insulator interactions are orientation-dependent. Consistent with a role in the alignment and pairing of homologs, self-pairing in trans is head-to-head. Head-to-head self-interactions in cis have been reported for other fly insulators, suggesting that this is a general principle of self-pairing. Homie and Nhomie not only pair with themselves, but with each other. Heterologous Homie-Nhomie interactions occur in cis, and we show that they serve to delimit a looped chromosomal domain that contains the even skipped transcription unit and its associated enhancers. The topology of this loop is defined by the heterologous pairing properties of Homie and Nhomie. Instead of being head-to-head, which would generate a circular loop, Homie-Nhomie pairing is head-to-tail. Head-to-tail pairing in cis generates a stem-loop, a configuration much like that observed in classical lampbrush chromosomes. These pairing principles provide a mechanistic underpinning for the observed topologies within and between chromosomes. The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible for both subdividing the chromatin fiber into discrete domains, and determining the topological organization of these domains. Central to the architectural functions of insulators are heterologous and homologous insulator:insulator pairing interactions. In Drosophila, the former defines the topology of individual looped domains in cis, while the latter dictates the process of homolog alignment and pairing in trans. Here we use two insulators from the even skipped locus to elucidate the principles governing these two architectural functions. These principles align with several longstanding observations, and resolve a number of conundrums regarding chromosome topology and function.
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Affiliation(s)
- Miki Fujioka
- Deptartment of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Hemlata Mistry
- Departments of Biology and Biochemistry, Widener University, Chester, Pennsylvania, United States of America
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (PS); (JBJ)
| | - James B. Jaynes
- Deptartment of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (PS); (JBJ)
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30
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Powers NR, Eicher JD, Miller LL, Kong Y, Smith SD, Pennington BF, Willcutt EG, Olson RK, Ring SM, Gruen JR. The regulatory element READ1 epistatically influences reading and language, with both deleterious and protective alleles. J Med Genet 2015; 53:163-71. [PMID: 26660103 PMCID: PMC4789805 DOI: 10.1136/jmedgenet-2015-103418] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/14/2015] [Indexed: 01/05/2023]
Abstract
Background Reading disability (RD) and language impairment (LI) are heritable learning disabilities that obstruct acquisition and use of written and spoken language, respectively. We previously reported that two risk haplotypes, each in strong linkage disequilibrium (LD) with an allele of READ1, a polymorphic compound short tandem repeat within intron 2 of risk gene DCDC2, are associated with RD and LI. Additionally, we showed a non-additive genetic interaction between READ1 and KIAHap, a previously reported risk haplotype in risk gene KIAA0319, and that READ1 binds the transcriptional regulator ETV6. Objective To examine the hypothesis that READ1 is a transcriptional regulator of KIAA0319. Methods We characterised associations between READ1 alleles and RD and LI in a large European cohort, and also assessed interactions between READ1 and KIAHap and their effect on performance on measures of reading, language and IQ. We also used family-based data to characterise the genetic interaction, and chromatin conformation capture (3C) to investigate the possibility of a physical interaction between READ1 and KIAHap. Results and conclusions READ1 and KIAHap show interdependence—READ1 risk alleles synergise with KIAHap, whereas READ1 protective alleles act epistatically to negate the effects of KIAHap. The family data suggest that these variants interact in trans genetically, while the 3C results show that a region of DCDC2 containing READ1 interacts physically with the region upstream of KIAA0319. These data support a model in which READ1 regulates KIAA0319 expression through KIAHap and in which the additive effects of READ1 and KIAHap alleles are responsible for the trans genetic interaction.
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Affiliation(s)
- Natalie R Powers
- Investigate Medicine, Yale University, New Haven, Connecticut, USA Department of Pediatrics, Yale University, New Haven, Connecticut, USA
| | - John D Eicher
- Investigate Medicine, Yale University, New Haven, Connecticut, USA
| | - Laura L Miller
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut, USA
| | - Shelley D Smith
- Departments of Pediatrics and Developmental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | | | - Erik G Willcutt
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA Departments of Psychology and Neuroscience, University of Colorado, Boulder, Colorado, USA
| | - Richard K Olson
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA Departments of Psychology and Neuroscience, University of Colorado, Boulder, Colorado, USA
| | - Susan M Ring
- School of Social and Community Medicine, University of Bristol, Bristol, UK MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Jeffrey R Gruen
- Investigate Medicine, Yale University, New Haven, Connecticut, USA Department of Pediatrics, Yale University, New Haven, Connecticut, USA Department of Investigative Medicine, Yale University, New Haven, Connecticut, USA
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31
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Sex Differences in Drosophila melanogaster Heterochromatin Are Regulated by Non-Sex Specific Factors. PLoS One 2015; 10:e0128114. [PMID: 26053165 PMCID: PMC4459879 DOI: 10.1371/journal.pone.0128114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/22/2015] [Indexed: 12/26/2022] Open
Abstract
The eukaryotic genome is assembled into distinct types of chromatin. Gene-rich euchromatin has active chromatin marks, while heterochromatin is gene-poor and enriched for silencing marks. In spite of this, genes native to heterochromatic regions are dependent on their normal environment for full expression. Expression of genes in autosomal heterochromatin is reduced in male flies mutated for the noncoding roX RNAs, but not in females. roX mutations also disrupt silencing of reporter genes in male, but not female, heterochromatin, revealing a sex difference in heterochromatin. We adopted a genetic approach to determine how this difference is regulated, and found no evidence that known X chromosome counting elements, or the sex determination pathway that these control, are involved. This suggested that the sex chromosome karyotype regulates autosomal heterochromatin by a different mechanism. To address this, candidate genes that regulate chromosome organization were examined. In XX flies mutation of Topoisomerase II (Top2), a gene involved in chromatin organization and homolog pairing, made heterochromatic silencing dependent on roX, and thus male-like. Interestingly, Top2 also binds to a large block of pericentromeric satellite repeats (359 bp repeats) that are unique to the X chromosome. Deletion of X heterochromatin also makes autosomal heterochromatin in XX flies dependent on roX and enhances the effect of Top2 mutations, suggesting a combinatorial action. We postulate that Top2 and X heterochromatin in Drosophila comprise a novel karyotype-sensing pathway that determines the sensitivity of autosomal heterochromatin to loss of roX RNA.
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Sass GL, Ostrow BD. Disruption of the protein kinase N gene of drosophila melanogaster results in the recessive delorean allele (pkndln) with a negative impact on wing morphogenesis. G3 (BETHESDA, MD.) 2014; 4:643-56. [PMID: 24531729 PMCID: PMC4059237 DOI: 10.1534/g3.114.010579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/07/2014] [Indexed: 12/15/2022]
Abstract
We describe the delorean mutation of the Drosophila melanogaster protein kinase N gene (pkn(dln)) with defects in wing morphology. Flies homozygous for the recessive pkn(dln) allele have a composite wing phenotype that exhibits changes in relative position and shape of the wing blade as well as loss of specific vein and bristle structures. The pkn(dln) allele is the result of a P-element insertion in the first intron of the pkn locus, and the delorean wing phenotype is contingent upon the interaction of insertion-bearing alleles in trans. The presence of the insertion results in production of a novel transcript that initiates from within the 3' end of the P-element. The delorean-specific transcript is predicted to produce a wild-type PKN protein. The delorean phenotype is not the result of a reduction in pkn expression, as it could not be recreated using a variety of wing-specific drivers of pkn-RNAi expression. Rather, it is the presence of the delorean-specific transcript that correlates with the mutant phenotype. We consider the delorean wing phenotype to be due to a pairing-dependent, recessive mutation that behaves as a dosage-sensitive, gain of function. Our analysis of genetic interactions with basket and nemo reflects an involvement of pkn and Jun-terminal kinase signaling in common processes during wing differentiation and places PKN as a potential effector of Rho1's involvement in the Jun-terminal kinase pathway. The delorean phenotype, with its associated defects in wing morphology, provides evidence of a role for PKN in adult morphogenetic processes.
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Affiliation(s)
- Georgette L. Sass
- Department of Biology, Grand Valley State University, Allendale, Michigan 49401
| | - Bruce D. Ostrow
- Department of Biology, Grand Valley State University, Allendale, Michigan 49401
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33
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Gladyshev E, Kleckner N. Direct recognition of homology between double helices of DNA in Neurospora crassa. Nat Commun 2014; 5:3509. [PMID: 24699390 PMCID: PMC4000310 DOI: 10.1038/ncomms4509] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/25/2014] [Indexed: 12/11/2022] Open
Abstract
Chromosomal regions of identical or nearly identical DNA sequence can preferentially associate with one another in the apparent absence of DNA breakage. Molecular mechanism(s) underlying such homology-dependent pairing phenomena remain(s) unknown. Using Neurospora crassa repeat-induced point mutation (RIP) as a model system, we show that a pair of DNA segments can be recognized as homologous if they share triplets of base pairs arrayed with the matching periodicity of 11 or 12 base pairs. This pattern suggests direct interactions between slightly underwound co-aligned DNA duplexes engaging once per turn and over many consecutive turns. The process occurs in the absence of MEI3, the only RAD51/DMC1 protein in N. crassa, demonstrating independence from the canonical homology recognition pathway. A new perspective is thus provided for further analysis of the breakage-independent recognition of homology that underlies RIP and, potentially, other processes where sequence-specific pairing of intact chromosomes is involved.
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Affiliation(s)
- Eugene Gladyshev
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Room NW140, Cambridge, Massachusetts 02138, USA
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Room NW140, Cambridge, Massachusetts 02138, USA
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34
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Joyce EF, Apostolopoulos N, Beliveau BJ, Wu CT. Germline progenitors escape the widespread phenomenon of homolog pairing during Drosophila development. PLoS Genet 2013; 9:e1004013. [PMID: 24385920 PMCID: PMC3868550 DOI: 10.1371/journal.pgen.1004013] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/24/2013] [Indexed: 01/06/2023] Open
Abstract
Homolog pairing, which plays a critical role in meiosis, poses a potential risk if it occurs in inappropriate tissues or between nonallelic sites, as it can lead to changes in gene expression, chromosome entanglements, and loss-of-heterozygosity due to mitotic recombination. This is particularly true in Drosophila, which supports organismal-wide pairing throughout development. Discovered over a century ago, such extensive pairing has led to the perception that germline pairing in the adult gonad is an extension of the pairing established during embryogenesis and, therefore, differs from the mechanism utilized in most species to initiate pairing specifically in the germline. Here, we show that, contrary to long-standing assumptions, Drosophila meiotic pairing in the gonad is not an extension of pairing established during embryogenesis. Instead, we find that homologous chromosomes are unpaired in primordial germ cells from the moment the germline can be distinguished from the soma in the embryo and remain unpaired even in the germline stem cells of the adult gonad. We further establish that pairing originates immediately after the stem cell stage. This pairing occurs well before the initiation of meiosis and, strikingly, continues through the several mitotic divisions preceding meiosis. These discoveries indicate that the spatial organization of the Drosophila genome differs between the germline and the soma from the earliest moments of development and thus argue that homolog pairing in the germline is an active process as versus a passive continuation of pairing established during embryogenesis. Meiosis is a specialized cell division that permits the transmission of genetic material to following generations. A pivotal step for this process is the pairing and recombination between homologous chromosomes. In the case of Drosophila, which supports organismal-wide homolog pairing throughout development, it has been widely assumed that the homolog alignment occurring during meiosis in the adult gonad is an extension of the pairing established during embryogenesis. Here, we show that, contrary to this model, homologous chromosomes are unpaired in germline progenitors from embryogenesis to adulthood. This discovery refutes the presumption that homologous chromosomes are paired in Drosophila in all cell types and demonstrates that a specific form of chromosome organization, namely, homolog pairing, is a signature feature that distinguishes cells destined to be the soma from cells destined to be the germline.
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Affiliation(s)
- Eric F Joyce
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nicholas Apostolopoulos
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Brian J Beliveau
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - C-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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35
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Wallace HA, Bosco G. Condensins and 3D Organization of the Interphase Nucleus. CURRENT GENETIC MEDICINE REPORTS 2013; 1:219-229. [PMID: 24563825 DOI: 10.1007/s40142-013-0024-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Condensins are conserved multi-subunit protein complexes that participate in eukaryotic genome organization. Well known for their role in mitotic chromosome condensation, condensins have recently emerged as integral components of diverse interphase processes. Recent evidence shows that condensins are involved in chromatin organization, gene expression, and DNA repair and indicates similarities between the interphase and mitotic functions of condensin. Recent work has enhanced our knowledge of how chromatin architecture is dynamically regulated by condensin to impact essential cellular processes.
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Affiliation(s)
- Heather A Wallace
- Department of Genetics, Geisel School of Medicine at Dartmouth, 609 Vail, HB 7400, Hanover, NH 03755, USA
| | - Giovanni Bosco
- Department of Genetics, Geisel School of Medicine at Dartmouth, 609 Vail, HB 7400, Hanover, NH 03755, USA
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