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Hu C, Zhu XT, He MH, Shao Y, Qin Z, Wu ZJ, Zhou JQ. Elimination of subtelomeric repeat sequences exerts little effect on telomere essential functions in Saccharomyces cerevisiae. eLife 2024; 12:RP91223. [PMID: 38656297 DOI: 10.7554/elife.91223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Telomeres, which are chromosomal end structures, play a crucial role in maintaining genome stability and integrity in eukaryotes. In the baker's yeast Saccharomyces cerevisiae, the X- and Y'-elements are subtelomeric repetitive sequences found in all 32 and 17 telomeres, respectively. While the Y'-elements serve as a backup for telomere functions in cells lacking telomerase, the function of the X-elements remains unclear. This study utilized the S. cerevisiae strain SY12, which has three chromosomes and six telomeres, to investigate the role of X-elements (as well as Y'-elements) in telomere maintenance. Deletion of Y'-elements (SY12YΔ), X-elements (SY12XYΔ+Y), or both X- and Y'-elements (SY12XYΔ) did not impact the length of the terminal TG1-3 tracks or telomere silencing. However, inactivation of telomerase in SY12YΔ, SY12XYΔ+Y, and SY12XYΔ cells resulted in cellular senescence and the generation of survivors. These survivors either maintained their telomeres through homologous recombination-dependent TG1-3 track elongation or underwent microhomology-mediated intra-chromosomal end-to-end joining. Our findings indicate the non-essential role of subtelomeric X- and Y'-elements in telomere regulation in both telomerase-proficient and telomerase-null cells and suggest that these elements may represent remnants of S. cerevisiae genome evolution. Furthermore, strains with fewer or no subtelomeric elements exhibit more concise telomere structures and offer potential models for future studies in telomere biology.
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Affiliation(s)
- Can Hu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Xue-Ting Zhu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Ming-Hong He
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Yangyang Shao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhongjun Qin
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhi-Jing Wu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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2
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Ghimire P, Motamedi M, Joh R. Mathematical model for the role of multiple pericentromeric repeats on heterochromatin assembly. PLoS Comput Biol 2024; 20:e1012027. [PMID: 38598558 PMCID: PMC11034663 DOI: 10.1371/journal.pcbi.1012027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 04/22/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Although the length and constituting sequences for pericentromeric repeats are highly variable across eukaryotes, the presence of multiple pericentromeric repeats is one of the conserved features of the eukaryotic chromosomes. Pericentromeric heterochromatin is often misregulated in human diseases, with the expansion of pericentromeric repeats in human solid cancers. In this article, we have developed a mathematical model of the RNAi-dependent methylation of H3K9 in the pericentromeric region of fission yeast. Our model, which takes copy number as an explicit parameter, predicts that the pericentromere is silenced only if there are many copies of repeats. It becomes bistable or desilenced if the copy number of repeats is reduced. This suggests that the copy number of pericentromeric repeats alone can determine the fate of heterochromatin silencing in fission yeast. Through sensitivity analysis, we identified parameters that favor bistability and desilencing. Stochastic simulation shows that faster cell division and noise favor the desilenced state. These results show the unexpected role of pericentromeric repeat copy number in gene silencing and provide a quantitative basis for how the copy number allows or protects repetitive and unique parts of the genome from heterochromatin silencing, respectively.
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Affiliation(s)
- Puranjan Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Mo Motamedi
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, Boston, Massachusetts, United States of America
| | - Richard Joh
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Massey Cancer Center, Virginia Commonwealth University, Richmond Virginia, United States of America
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3
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Schmidt N, Sielemann K, Breitenbach S, Fuchs J, Pucker B, Weisshaar B, Holtgräwe D, Heitkam T. Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets. Plant J 2024; 118:171-190. [PMID: 38128038 DOI: 10.1111/tpj.16599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Sugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome-wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.
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Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
| | - Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Sarah Breitenbach
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, 38106, Braunschweig, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Graz, Austria
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4
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Pliota P, Marvanova H, Koreshova A, Kaufman Y, Tikanova P, Krogull D, Hagmüller A, Widen SA, Handler D, Gokcezade J, Duchek P, Brennecke J, Ben-David E, Burga A. Selfish conflict underlies RNA-mediated parent-of-origin effects. Nature 2024; 628:122-129. [PMID: 38448590 PMCID: PMC10990930 DOI: 10.1038/s41586-024-07155-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/02/2024] [Indexed: 03/08/2024]
Abstract
Genomic imprinting-the non-equivalence of maternal and paternal genomes-is a critical process that has evolved independently in many plant and mammalian species1,2. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles3,4. Yet, how these epigenetic differences evolve in the first place is poorly understood3,5,6. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals7-9. In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs-but not SLOW-1 protein-are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.
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Affiliation(s)
- Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Hana Marvanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Yotam Kaufman
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Polina Tikanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Andreas Hagmüller
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Joseph Gokcezade
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Eyal Ben-David
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
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5
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Nguyen MTA, Gobry MV, Sampedro Vallina N, Pothoulakis G, Andersen ES. Enzymatic Assembly of Small Synthetic Genes with Repetitive Elements. ACS Synth Biol 2024; 13:963-968. [PMID: 38437525 PMCID: PMC10949351 DOI: 10.1021/acssynbio.3c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 03/06/2024]
Abstract
Gene synthesis efficiency has greatly improved in recent years but is limited when it comes to repetitive sequences, which results in synthesis failure or delays by DNA synthesis vendors. This represents a major obstacle for the development of synthetic biology since repetitive elements are increasingly being used in the design of genetic circuits and design of biomolecular nanostructures. Here, we describe a method for the assembly of small synthetic genes with repetitive elements: First, a gene of interest is split in silico into small synthons of up to 80 base pairs flanked by Golden-Gate-compatible overhangs. Then, synthons are made by oligo extension and finally assembled into a synthetic gene by Golden Gate Assembly. We demonstrate the method by constructing eight challenging genes with repetitive elements, e.g., multiple repeats of RNA aptamers and RNA origami scaffolds with multiple identical aptamers. The genes range in size from 133 to 456 base pairs and are assembled with fidelities of up to 87.5%. The method was developed to facilitate our own specific research but may be of general use for constructing challenging and repetitive genes and, thus, a valuable addition to the molecular cloning toolbox.
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Affiliation(s)
- Michael T. A. Nguyen
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
| | - Martin Vincent Gobry
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
| | - Néstor Sampedro Vallina
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
| | - Georgios Pothoulakis
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
| | - Ebbe Sloth Andersen
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
- Department
of Molecular Biology and Genetics, Aarhus
University, Gustav Wieds
Vej 14, DK-8000 Aarhus, Denmark
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6
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Trajkovski M, Pastore A, Plavec J. Dimeric structures of DNA ATTTC repeats promoted by divalent cations. Nucleic Acids Res 2024; 52:1591-1601. [PMID: 38296828 PMCID: PMC10899783 DOI: 10.1093/nar/gkae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
Structural studies of repetitive DNA sequences may provide insights why and how certain repeat instabilities in their number and nucleotide sequence are managed or even required for normal cell physiology, while genomic variability associated with repeat expansions may also be disease-causing. The pentanucleotide ATTTC repeats occur in hundreds of genes important for various cellular processes, while their insertion and expansion in noncoding regions are associated with neurodegeneration, particularly with subtypes of spinocerebellar ataxia and familial adult myoclonic epilepsy. We describe a new striking domain-swapped DNA-DNA interaction triggered by the addition of divalent cations, including Mg2+ and Ca2+. The results of NMR characterization of d(ATTTC)3 in solution show that the oligonucleotide folds into a novel 3D architecture with two central C:C+ base pairs sandwiched between a couple of T:T base pairs. This structural element, referred to here as the TCCTzip, is characterized by intercalative hydrogen-bonding, while the nucleobase moieties are poorly stacked. The 5'- and 3'-ends of TCCTzip motif are connected by stem-loop segments characterized by A:T base pairs and stacking interactions. Insights embodied in the non-canonical DNA structure are expected to advance our understanding of why only certain pyrimidine-rich DNA repeats appear to be pathogenic, while others can occur in the human genome without any harmful consequences.
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Affiliation(s)
- Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Annalisa Pastore
- King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
- EN-FIST, Center of Excellence, 1000 Ljubljana, Slovenia
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7
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Aguilar R, Camplisson CK, Lin Q, Miga KH, Noble WS, Beliveau BJ. Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes. Nat Commun 2024; 15:1027. [PMID: 38310092 PMCID: PMC10838309 DOI: 10.1038/s41467-024-45385-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
Fluorescent in situ hybridization (FISH) is a powerful method for the targeted visualization of nucleic acids in their native contexts. Recent technological advances have leveraged computationally designed oligonucleotide (oligo) probes to interrogate > 100 distinct targets in the same sample, pushing the boundaries of FISH-based assays. However, even in the most highly multiplexed experiments, repetitive DNA regions are typically not included as targets, as the computational design of specific probes against such regions presents significant technical challenges. Consequently, many open questions remain about the organization and function of highly repetitive sequences. Here, we introduce Tigerfish, a software tool for the genome-scale design of oligo probes against repetitive DNA intervals. We showcase Tigerfish by designing a panel of 24 interval-specific repeat probes specific to each of the 24 human chromosomes and imaging this panel on metaphase spreads and in interphase nuclei. Tigerfish extends the powerful toolkit of oligo-based FISH to highly repetitive DNA.
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Affiliation(s)
- Robin Aguilar
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Conor K Camplisson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Qiaoyi Lin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
| | - Brian J Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
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8
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Monier M, Nuez I, Borne F, Courtier-Orgogozo V. Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences. BMC Ecol Evol 2024; 24:18. [PMID: 38308233 PMCID: PMC10835880 DOI: 10.1186/s12862-023-02178-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 11/23/2023] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND During evolution, genes can experience duplications, losses, inversions and gene conversions. Why certain genes are more dynamic than others is poorly understood. Here we examine how several Sgs genes encoding glue proteins, which make up a bioadhesive that sticks the animal during metamorphosis, have evolved in Drosophila species. RESULTS We examined high-quality genome assemblies of 24 Drosophila species to study the evolutionary dynamics of four glue genes that are present in D. melanogaster and are part of the same gene family - Sgs1, Sgs3, Sgs7 and Sgs8 - across approximately 30 millions of years. We annotated a total of 102 Sgs genes and grouped them into 4 subfamilies. We present here a new nomenclature for these Sgs genes based on protein sequence conservation, genomic location and presence/absence of internal repeats. Two types of glue genes were uncovered. The first category (Sgs1, Sgs3x, Sgs3e) showed a few gene losses but no duplication, no local inversion and no gene conversion. The second group (Sgs3b, Sgs7, Sgs8) exhibited multiple events of gene losses, gene duplications, local inversions and gene conversions. Our data suggest that the presence of short "new glue" genes near the genes of the latter group may have accelerated their dynamics. CONCLUSIONS Our comparative analysis suggests that the evolutionary dynamics of glue genes is influenced by genomic context. Our molecular, phylogenetic and comparative analysis of the four glue genes Sgs1, Sgs3, Sgs7 and Sgs8 provides the foundation for investigating the role of the various glue genes during Drosophila life.
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Affiliation(s)
- Manon Monier
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013, Paris, France
| | - Isabelle Nuez
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013, Paris, France
| | - Flora Borne
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013, Paris, France
- Department of Biological Sciences, Columbia University, New York city, New York, USA
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9
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Kubickova S, Kopecna O, Cernohorska H, Rubes J, Vozdova M. X Chromosome-Specific Repeats in Non-Domestic Bovidae. Genes (Basel) 2024; 15:159. [PMID: 38397149 PMCID: PMC10887555 DOI: 10.3390/genes15020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Repetitive sequences form a substantial and still enigmatic part of the mammalian genome. We isolated repetitive DNA blocks of the X chromosomes of three species of the family Bovidae: Kobus defassa (KDEXr sequence), Bos taurus (BTAXr sequence) and Antilope cervicapra (ACEXr sequence). The copy numbers of the isolated sequences were assessed using qPCR, and their chromosomal localisations were analysed using FISH in ten bovid tribes and in outgroup species. Besides their localisation on the X chromosome, their presence was also revealed on the Y chromosome and autosomes in several species. The KDEXr sequence abundant in most Bovidae species also occurs in distant taxa (Perissodactyla and Carnivora) and seems to be evolutionarily older than BTAXr and ACEXr. The ACEXr sequence, visible only in several Antilopini species using FISH, is probably the youngest, and arised in an ancestor common to Bovidae and Cervidae. All three repetitive sequences analysed in this study are interspersed among gene-rich regions on the X chromosomes, apparently preventing the crossing-over in their close vicinity. This study demonstrates that repetitive sequences on the X chromosomes have undergone a fast evolution, and their variation among related species can be beneficial for evolutionary studies.
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Affiliation(s)
| | | | | | | | - Miluse Vozdova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.R.)
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10
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Shiekh S, Kodikara SG, Balci H. Structure, Topology, and Stability of Multiple G-quadruplexes in Long Telomeric Overhangs. J Mol Biol 2024; 436:168205. [PMID: 37481156 PMCID: PMC10799177 DOI: 10.1016/j.jmb.2023.168205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Telomeres and their single stranded overhangs gradually shorten with successive cell divisions, as part of the natural aging process, but can be elongated by telomerase, a nucleoprotein complex which is activated in the majority of cancers. This prominent implication in cancer and aging has made the repetitive telomeric sequences (TTAGGG repeats) and the G-quadruplex structures that form in their overhangs the focus of intense research in the past several decades. However, until recently most in vitro efforts to understand the structure, stability, dynamics, and interactions of telomeric overhangs had been focused on short sequences that are not representative of longer sequences encountered in a physiological setting. In this review, we will provide a broad perspective about telomeres and associated factors, and introduce the agents and structural characteristics involved in organizing, maintaining, and protecting telomeric DNA. We will also present a summary of recent research performed on long telomeric sequences, nominally defined as those that can form two or more tandem G-quadruplexes, i.e., which contain eight or more TTAGGG repeats. Results of experimental studies using a broad array of experimental tools, in addition to recent computational efforts will be discussed, particularly in terms of their implications for the stability, folding topology, and compactness of the tandem G-quadruplexes that form in long telomeric overhangs.
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Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA.
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11
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She H, Liu Z, Li S, Xu Z, Zhang H, Cheng F, Wu J, Wang X, Deng C, Charlesworth D, Gao W, Qian W. Evolution of the spinach sex-linked region within a rarely recombining pericentromeric region. Plant Physiol 2023; 193:1263-1280. [PMID: 37403642 DOI: 10.1093/plphys/kiad389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/06/2023]
Abstract
Sex chromosomes have evolved independently in many different plant lineages. Here, we describe reference genomes for spinach (Spinacia oleracea) X and Y haplotypes by sequencing homozygous XX females and YY males. The long arm of 185-Mb chromosome 4 carries a 13-Mb X-linked region (XLR) and 24.1-Mb Y-linked region (YLR), of which 10 Mb is Y specific. We describe evidence that this reflects insertions of autosomal sequences creating a "Y duplication region" or "YDR" whose presence probably directly reduces genetic recombination in the immediately flanking regions, although both the X and Y sex-linked regions are within a large pericentromeric region of chromosome 4 that recombines rarely in meiosis of both sexes. Sequence divergence estimates using synonymous sites indicate that YDR genes started diverging from their likely autosomal progenitors about 3 MYA, around the time when the flanking YLR stopped recombining with the XLR. These flanking regions have a higher density of repetitive sequences in the YY than the XX assembly and include slightly more pseudogenes compared with the XLR, and the YLR has lost about 11% of the ancestral genes, suggesting some degeneration. Insertion of a male-determining factor would have caused Y linkage across the entire pericentromeric region, creating physically small, highly recombining, terminal pseudoautosomal regions. These findings provide a broader understanding of the origin of sex chromosomes in spinach.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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12
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Saayman X, Graham E, Leung CWB, Esashi F. exo-FISH: Protocol for detecting DNA breaks in repetitive regions of mammalian genomes. STAR Protoc 2023; 4:102487. [PMID: 37549036 PMCID: PMC10425934 DOI: 10.1016/j.xpro.2023.102487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/07/2023] [Accepted: 07/12/2023] [Indexed: 08/09/2023] Open
Abstract
Detecting DNA breaks in defined regions of the genome is critical to advancing our understanding of genome stability maintenance. Here, we present exo-FISH, a protocol to label exposed single-stranded DNA in defined repetitive regions of mammalian genomes by combining in vitro restriction enzyme digestion on fixed cells with fluorescence in situ hybridization (FISH). We describe steps for cell harvesting and fixation, slide treatments, and FISH probe hybridization. We then detail procedures for imaging and analysis. For complete details on the use and execution of this protocol, please refer to Saayman et al. (2023).1.
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Affiliation(s)
- Xanita Saayman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| | - Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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13
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Uno Y, Matsubara K, Inoue J, Inazawa J, Shinohara A, Koshimoto C, Ichiyanagi K, Matsuda Y. Diversity and Evolution of Highly Repetitive DNA Sequences Constituting Chromosome Site-Specific Heterochromatin in Two Gerbillinae Species. Cytogenet Genome Res 2023; 163:42-51. [PMID: 37708873 DOI: 10.1159/000533716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023] Open
Abstract
Constitutive heterochromatin, consisting of repetitive sequences, diverges very rapidly; therefore, its nucleotide sequences and chromosomal distributions are often largely different, even between closely related species. The chromosome C-banding patterns of two Gerbillinae species, Meriones unguiculatus and Gerbillus perpallidus, vary greatly, even though they belong to the same subfamily. To understand the evolution of C-positive heterochromatin in these species, we isolated highly repetitive sequences, determined their nucleotide sequences, and characterized them using chromosomal and filter hybridization. We obtained a centromeric repeat (MUN-HaeIII) and a chromosome 13-specific repeat (MUN-EcoRI) from M. unguiculatus. We also isolated a centromeric/pericentromeric repeat (GPE-MBD) and an interspersed-type repeat that was predominantly amplified in the X and Y chromosomes (GPE-EcoRI) from G. perpallidus. GPE-MBD was found to contain a 17-bp motif that is essential for binding to the centromere-associated protein CENP-B. This indicates that it may play a role in the formation of a specified structure and/or function of centromeres. The nucleotide sequences of the three sequence families, except GPE-EcoRI, were conserved only in Gerbillinae. GPE-EcoRI was derived from the long interspersed nuclear elements 1 retrotransposon and showed sequence homology throughout Muridae and Cricetidae species, indicating that the repeat sequence occurred at least in the common ancestor of Muridae and Cricetidae. Due to a lack of assembly data of highly repetitive sequences constituting heterochromatin in whole-genome sequences of vertebrate species published to date, the knowledge obtained in this study provides useful information for a deep understanding of the evolution of repetitive sequences in not only rodents but also in mammals.
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Affiliation(s)
- Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazumi Matsubara
- Department of Environmental Biology, College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Jun Inoue
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akio Shinohara
- Department of Biotechnology, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Chihiro Koshimoto
- Department of Biotechnology, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Kenji Ichiyanagi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yoichi Matsuda
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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14
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Zürcher JF, Kleefeldt AA, Funke LFH, Birnbaum J, Fredens J, Grazioli S, Liu KC, Spinck M, Petris G, Murat P, Rehm FBH, Sale JE, Chin JW. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature 2023; 619:555-562. [PMID: 37380776 PMCID: PMC7614783 DOI: 10.1038/s41586-023-06268-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Whole-genome synthesis provides a powerful approach for understanding and expanding organism function1-3. To build large genomes rapidly, scalably and in parallel, we need (1) methods for assembling megabases of DNA from shorter precursors and (2) strategies for rapidly and scalably replacing the genomic DNA of organisms with synthetic DNA. Here we develop bacterial artificial chromosome (BAC) stepwise insertion synthesis (BASIS)-a method for megabase-scale assembly of DNA in Escherichia coli episomes. We used BASIS to assemble 1.1 Mb of human DNA containing numerous exons, introns, repetitive sequences, G-quadruplexes, and long and short interspersed nuclear elements (LINEs and SINEs). BASIS provides a powerful platform for building synthetic genomes for diverse organisms. We also developed continuous genome synthesis (CGS)-a method for continuously replacing sequential 100 kb stretches of the E. coli genome with synthetic DNA; CGS minimizes crossovers1,4 between the synthetic DNA and the genome such that the output for each 100 kb replacement provides, without sequencing, the input for the next 100 kb replacement. Using CGS, we synthesized a 0.5 Mb section of the E. coli genome-a key intermediate in its total synthesis1-from five episomes in 10 days. By parallelizing CGS and combining it with rapid oligonucleotide synthesis and episome assembly5,6, along with rapid methods for compiling a single genome from strains bearing distinct synthetic genome sections1,7,8, we anticipate that it will be possible to synthesize entire E. coli genomes from functional designs in less than 2 months.
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Affiliation(s)
- Jérôme F Zürcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Askar A Kleefeldt
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Louise F H Funke
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Jakob Birnbaum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julius Fredens
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Synthetic Biology for Clinical and Technological Innovation, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Simona Grazioli
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Martin Spinck
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Pierre Murat
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fabian B H Rehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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15
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Gorobeyko UV, Sheremetyeva IN, Kazakov DV, Guskov VY. A new type of tandem repeats in Myotis petax (Chiroptera, Vespertilionidae) mitochondrial control region. Mol Biol Rep 2023; 50:5137-5146. [PMID: 37115485 DOI: 10.1007/s11033-023-08468-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/18/2023] [Indexed: 04/29/2023]
Abstract
BACKGROUND Tandem repeats in mitochondrial DNA control region are known to different animal taxa, including bat species of the family Vespertilionidae. The long R1-repeats in the bat ETAS-domain are often presented in a variable copy number and may exhibit both inter-individual and intra-individual sequence diversity. The function of repeats in the control region is still unclear, but it has been shown that repetitive sequences in some animal groups (shrews, cats and sheep) may include parts of ETAS1 and ETAS2 conservative blocks of mitochondrial DNA. METHODS AND RESULTS Analysis of the control region sequences for 31 Myotis petax specimens allowed the identification of the inter-individual variability and clarification of the composition of the R1-repeats. The copy number of the R1-repeats varies from 4 to 7 in individuals. The specimens examined do not exhibit a size heteroplasmy previously described for Myotis species. The unusual short 30 bp R1-repeats have been detected in M. petax for the first time. The ten specimens from Amur Region and Primorsky Territory have one or two copies of these additional repeats. CONCLUSIONS It was determined that the R1-repeats in M. petax control region consist of parts of the ETAS1 and ETAS2 blocks. The origin of the additional repeats seems to be related to the 51 bp deletion in the central part of the R1-repeat unit and subsequent duplication. Comparison of repetitive sequences in the control region of closely-related Myotis species identified the occurrence of incomplete repeats also resulting from the short deletions, but distinct from additional repeats of M. petax.
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Affiliation(s)
- Uliana Vasilievna Gorobeyko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, 159 Prospect Stoletiya St., Vladivostok, 690022, Russia.
| | - Irina Nikolaevna Sheremetyeva
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, 159 Prospect Stoletiya St., Vladivostok, 690022, Russia
| | - Denis Vasilievich Kazakov
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 6 Volodarskogo St., Tyumen, 625003, Russia
| | - Valentin Yurievich Guskov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, 159 Prospect Stoletiya St., Vladivostok, 690022, Russia
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16
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Kamimura E, Uno Y, Yamada K, Nishida C, Matsuda Y. Molecular Cytogenetic Characterization of C-Band-Positive Heterochromatin of the Greater Long-Tailed Hamster (<b><i>Tscherskia triton</i></b>, Cricetinae). Cytogenet Genome Res 2022; 162:323-333. [PMID: 36535261 DOI: 10.1159/000527478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/02/2022] [Indexed: 12/23/2022] Open
Abstract
The greater long-tailed hamster (<i>Tscherskia triton</i>, Cricetinae) has a unique karyotype (2n = 28), containing 11 pairs of acrocentric chromosomes with large C-band-positive centromeric heterochromatin blocks. To understand the origin and evolutionary process of heterochromatin in this species, we isolated novel families of chromosome site-specific highly repetitive DNA sequences from <i>Taq</i>I-digested genomic DNA and then characterized them by chromosome in situ and filter hybridization. The <i>Taq</i>I-families of repetitive sequences were classified into 2 types by their genome organization and chromosomal distribution: the 110-bp repeated sequence organized in large tandem arrays (as satellite DNA), localized to centromeric C-positive heterochromatin of acrocentric autosomes (chromosomes 1–11) and submetacentric X chromosome, and the 405-bp repeated sequence that was composed of 30–32-bp internal repeats, distributed in the pericentromeric region on the short arms of X and Y chromosomes. The repetitive sequences did not cross-hybridize with genomic DNA of any genera of Cricetinae (<i>Mesocricetus</i>, <i>Cricetulus</i>, and <i>Phodopus</i>). These results suggest that the 110-bp and 405-bp repeats rapidly diverged in the lineage of <i>T. triton</i>, evolving in a concerted manner among autosomes and X chromosome and within X and Y chromosomes, respectively. The 110-bp centromeric repeat contained a 17-bp motif in which 9 bases are essential for binding with the centromere-associated protein CENP-B, suggesting the possibility that the 110-bp major satellite DNA carrying the 17-bp motif may have a role in the formation of specified structure and/or function of centromeres in <i>T. triton</i>.
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Affiliation(s)
- Eikichi Kamimura
- Institute for Experimental Animals, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Yamada
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Chizuko Nishida
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Yoichi Matsuda
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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17
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Kolesnikova TD, Klenov MS, Nokhova AR, Lavrov SA, Pokholkova GV, Schubert V, Maltseva SV, Cook KR, Dixon MJ, Zhimulev IF. A Spontaneous Inversion of the X Chromosome Heterochromatin Provides a Tool for Studying the Structure and Activity of the Nucleolus in Drosophila melanogaster. Cells 2022; 11:cells11233872. [PMID: 36497131 PMCID: PMC9736023 DOI: 10.3390/cells11233872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
The pericentromeric heterochromatin is largely composed of repetitive sequences, making it difficult to analyze with standard molecular biological methods. At the same time, it carries many functional elements with poorly understood mechanisms of action. The search for new experimental models for the analysis of heterochromatin is an urgent task. In this work, we used the Rif1 mutation, which suppresses the underreplication of all types of repeated sequences, to analyze heterochromatin regions in polytene chromosomes of Drosophila melanogaster. In the Rif1 background, we discovered and described in detail a new inversion, In(1)19EHet, which arose on a chromosome already carrying the In(1)sc8 inversion and transferred a large part of X chromosome heterochromatin, including the nucleolar organizer to a new euchromatic environment. Using nanopore sequencing and FISH, we have identified the eu- and heterochromatin breakpoints of In(1)19EHet. The combination of the new inversion and the Rif1 mutation provides a promising tool for studies of X chromosome heterochromatin structure, nucleolar organization, and the nucleolar dominance phenomenon. In particular, we found that, with the complete polytenization of rDNA repeats, the nucleolus consists of a cloud-like structure corresponding to the classical nucleolus of polytene chromosomes, as well as an unusual intrachromosomal structure containing alternating transcriptionally active and inactive regions.
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Affiliation(s)
- Tatyana D. Kolesnikova
- Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
| | - Mikhail S. Klenov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Alina R. Nokhova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergey A. Lavrov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | | | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany
| | - Svetlana V. Maltseva
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Kevin R. Cook
- Bloomington Drosophila Stock Center, Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Michael J. Dixon
- Bloomington Drosophila Stock Center, Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
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18
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Williams SL, Coster G. Cloning and expansion of repetitive DNA sequences. Methods Cell Biol 2022; 182:167-185. [PMID: 38359975 DOI: 10.1016/bs.mcb.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Repeat and structure-prone DNA sequences comprise a large proportion of the human genome. The instability of these sequences has been implicated in a range of diseases, including cancers and neurodegenerative disorders. However, the mechanism of pathogenicity is poorly understood. As such, further studies on repetitive DNA are required. Cloning and maintaining repeat-containing substrates is challenging due to their inherent ability to form non-B DNA secondary structures which are refractory to DNA polymerases and prone to undergo rearrangements. Here, we describe an approach to clone and expand tandem-repeat DNA without interruptions, thereby allowing for its manipulation and subsequent investigation.
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Affiliation(s)
- Sophie L Williams
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, London, United Kingdom
| | - Gideon Coster
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, London, United Kingdom.
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19
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Hao J, Liang Y, Su Y, Wang T. The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis. Genes (Basel) 2022; 13:genes13071287. [PMID: 35886070 PMCID: PMC9316493 DOI: 10.3390/genes13071287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 12/02/2022] Open
Abstract
Many plant mitochondrial (mt) genomes have been sequenced but few in ferns. Ophioglossum vulgatum represents a typical species of fern genus Ophioglossum with medicinal and scientific value. However, its mt genome structure remains to be characterized. This study assembled and annotated the complete O. vulgatum mt genome and presented its structural characters and repeat sequences firstly. Its mt and chloroplast (cp) transfer sequences were explored, and the phylogenetic significance of both mt and cp genomes was also evaluated at the family level. Our results showed that the complete mt genome of O. vulgatum is a single circular genome of 369,673 bp in length, containing 5000 dispersed repetitive sequences. Phylogenetic trees reconstructed from cp and mt genomes displayed similar topologies, but also showed subtle differences at certain nodes. There exist 4818 bp common gene fragments between cp and mt genomes, of which more than 70% are located in tRNA intergenic regions (in mt). In conclusion, we assembled the complete mt genome of O. vulgatum, identified its remarkable structural characters, and provided new insights on ferns. The complementary results derived from mt and cp phylogeny highlighted that some higher taxonomic-level phylogenetic relationships among ferns remain to be resolved.
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Affiliation(s)
- Jing Hao
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (J.H.); (Y.L.)
| | - Yingyi Liang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (J.H.); (Y.L.)
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, China
- Correspondence: (Y.S.); (T.W.)
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (J.H.); (Y.L.)
- Correspondence: (Y.S.); (T.W.)
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20
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Haws SA, Simandi Z, Barnett RJ, Phillips-Cremins JE. 3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome. Cell 2022; 185:2690-2707. [PMID: 35868274 DOI: 10.1016/j.cell.2022.06.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 12/16/2022]
Abstract
Nearly half of the human genome is comprised of diverse repetitive sequences ranging from satellite repeats to retrotransposable elements. Such sequences are susceptible to stepwise expansions, duplications, inversions, and recombination events which can compromise genome function. In this review, we discuss the higher-order folding mechanisms of compartmentalization and loop extrusion and how they shape, and are shaped by, heterochromatin. Using primarily mammalian model systems, we contrast mechanisms governing H3K9me3-mediated heterochromatinization of the repetitive genome and highlight emerging links between repetitive elements and chromatin folding.
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Affiliation(s)
- Spencer A Haws
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoltan Simandi
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - R Jordan Barnett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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21
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Jain C, Rhie A, Hansen NF, Koren S, Phillippy AM. Long-read mapping to repetitive reference sequences using Winnowmap2. Nat Methods 2022; 19:705-710. [PMID: 35365778 PMCID: PMC10510034 DOI: 10.1038/s41592-022-01457-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 03/17/2022] [Indexed: 01/10/2023]
Abstract
Approximately 5-10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often yield incorrect alignments and variant calls within long, near-identical repeats, as they remain vulnerable to allelic bias. In the presence of a nonreference allele within a repeat, a read sampled from that region could be mapped to an incorrect repeat copy. To address this limitation, we developed a new long-read mapping method, Winnowmap2, by using minimal confidently alignable substrings. Winnowmap2 computes each read mapping through a collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats. Our experiments highlight that Winnowmap2 successfully addresses the issue of allelic bias, enabling more accurate downstream variant calls in repetitive sequences.
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Affiliation(s)
- Chirag Jain
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India.
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA.
| | - Arang Rhie
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Nancy F Hansen
- Comparative Genomics Analysis Unit, National Human Genome Research Institute, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
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Bowater RP, Bohálová N, Brázda V. Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids. Int J Mol Sci 2022; 23:ijms23116171. [PMID: 35682854 PMCID: PMC9180970 DOI: 10.3390/ijms23116171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases.
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Affiliation(s)
- Richard P. Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Correspondence:
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Abstract
We re-annotated repeats of 459 plant genomes and released a new database: PlantRep ( http://www.plantrep.cn/ ). PlantRep sheds lights of repeat evolution and provides fundamental data for deep exploration of genome.
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Affiliation(s)
- Xizhi Luo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Shiyu Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- School of Agriculture, Sun Yat-sen University, Shenzhen, 518107, China.
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Abstract
Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these errors, but most rely on short-read alignment which is unreliable in repeat regions. Errors in such regions are therefore challenging to fix and often remain after short-read polishing. Here we introduce Polypolish, a new short-read polisher which uses all-per-read alignments to repair errors in repeat sequences that other polishers cannot. Polypolish performed well in benchmarking tests using both simulated and real reads, and it almost never introduced errors during polishing. The best results were achieved by using Polypolish in combination with other short-read polishers. Recent improvements in Oxford Nanopore Technologies sequencing platforms and assembly algorithms have made it easier than ever to generate complete bacterial genome sequences. However, Oxford Nanopore genome sequences suffer from errors that limit their utility in downstream analyses. To fix these errors, one can ‘polish’ the genome with Illumina sequencing, exploiting the fact that Oxford Nanopore and Illumina sequencing have different error profiles. There are several polishing tools which can fix most errors in an Oxford Nanopore genome, but they struggle with errors in repetitive regions of the genome. With this in mind, we have developed a polisher, Polypolish, which uses a novel approach that allows it to fix more errors in genomic repeats. Our results show that Polypolish is both effective at repairing sequence errors and very unlikely to introduce new errors. Polypolish can often fix errors that other polishers cannot and vice versa, so the best results come from using a combination of tools. Polypolish therefore has an important role in bacterial genome assembly methods that aim for the highest possible sequence accuracy.
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Affiliation(s)
- Ryan R. Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- * E-mail:
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Zeng C, Takeda A, Sekine K, Osato N, Fukunaga T, Hamada M. Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs. Methods Mol Biol 2022; 2509:315-340. [PMID: 35796972 DOI: 10.1007/978-1-0716-2380-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
With a large number of annotated non-coding RNAs (ncRNAs), repetitive sequences are found to constitute functional components (termed as repetitive elements) in ncRNAs that perform specific biological functions. Bioinformatics analysis is a powerful tool for improving our understanding of the role of repetitive elements in ncRNAs. This chapter summarizes recent findings that reveal the role of repetitive elements in ncRNAs. Furthermore, relevant bioinformatics approaches are systematically reviewed, which promises to provide valuable resources for studying the functional impact of repetitive elements on ncRNAs.
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Affiliation(s)
- Chao Zeng
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan.
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan.
| | - Atsushi Takeda
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Kotaro Sekine
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Naoki Osato
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Tsukasa Fukunaga
- Waseda Institute for Advanced Study, Waseda University, Tokyo, Japan
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan.
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan.
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Meng R, Zhang L, Zhou C, Liao K, Xiao P, Luo Q, Xu J, Cui Y, Hu X, Yan X. Genome Sequence of Chrysotila roscoffensis, a Coccolithphore Contributed to Global Biogeochemical Cycles. Genes (Basel) 2021; 13:genes13010040. [PMID: 35052381 PMCID: PMC8775090 DOI: 10.3390/genes13010040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 01/18/2023] Open
Abstract
Chrysotila is a genus of coccolithophores. Together with Emiliania, it is one of the representative genera in the Haptophyta which have been extensively studied. They are photosynthetic unicellular marine algae sharing the common characteristic of the production of CaCO3 platelets (coccoliths) on the surface of their cells and are crucial contributors to global biogeochemical cycles. Here, we report the genome assembly of Chrysotila roscoffensis. The assembled genome size was ~636 Mb distributed across 769 scaffolds with N50 of 1.63 Mb, and maximum contig length of ~2.6 Mb. Repetitive elements accounted for approximately 59% of the genome. A total of 23,341 genes were predicted from C. roscoffensis genome. The divergence time between C. roscoffensis and Emiliania huxleyi was estimated to be around 537.6 Mya. Gene families related to cytoskeleton, cellular motility and morphology, and ion transport were expanded. The genome of C. roscoffensis will provide a foundation for understanding the genetic and phenotypic diversification and calcification mechanisms of coccolithophores.
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Affiliation(s)
- Ran Meng
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China; (R.M.); (C.Z.)
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China
- School of Marine Science, Ningbo University, Ningbo 315211, China; (L.Z.); (K.L.); (P.X.); (Q.L.); (J.X.)
| | - Lin Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China; (L.Z.); (K.L.); (P.X.); (Q.L.); (J.X.)
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China; (R.M.); (C.Z.)
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China
| | - Kai Liao
- School of Marine Science, Ningbo University, Ningbo 315211, China; (L.Z.); (K.L.); (P.X.); (Q.L.); (J.X.)
| | - Peng Xiao
- School of Marine Science, Ningbo University, Ningbo 315211, China; (L.Z.); (K.L.); (P.X.); (Q.L.); (J.X.)
| | - Qijun Luo
- School of Marine Science, Ningbo University, Ningbo 315211, China; (L.Z.); (K.L.); (P.X.); (Q.L.); (J.X.)
| | - Jilin Xu
- School of Marine Science, Ningbo University, Ningbo 315211, China; (L.Z.); (K.L.); (P.X.); (Q.L.); (J.X.)
| | - Yanze Cui
- Novogene Bioinformatics Institute, Beijing 100083, China;
| | - Xiaodi Hu
- Novogene Bioinformatics Institute, Beijing 100083, China;
- Correspondence: (X.H.); (X.Y.); Tel.: +86-0574-87600458 (X.Y.); +86-0574-87600738 (X.H.)
| | - Xiaojun Yan
- School of Marine Science, Ningbo University, Ningbo 315211, China; (L.Z.); (K.L.); (P.X.); (Q.L.); (J.X.)
- School of Marine Science, Zhejiang Ocean University, Zhoushan 316022, China
- Correspondence: (X.H.); (X.Y.); Tel.: +86-0574-87600458 (X.Y.); +86-0574-87600738 (X.H.)
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Fang B, Li J, Zhao Q, Liang Y, Yu J. Assembly of the Complete Mitochondrial Genome of Chinese Plum ( Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites. Genes (Basel) 2021; 12:genes12121970. [PMID: 34946920 PMCID: PMC8701122 DOI: 10.3390/genes12121970] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite the significant progress that has been made in the genome sequencing of Prunus, this area of research has been lacking a systematic description of the mitochondrial genome of this genus for a long time. In this study, we assembled the mitochondrial genome of the Chinese plum (Prunus salicina) using Illumina and Oxford Nanopore sequencing data. The mitochondrial genome size of P. salicina was found to be 508,035 base pair (bp), which is the largest reported in the Rosaceae family to date, and P. salicina was shown to be 63,453 bp longer than sweet cherry (P. avium). The P. salicina mitochondrial genome contained 37 protein-coding genes (PCGs), 3 ribosomal RNA (rRNA) genes, and 16 transfer RNA (tRNA) genes. Two plastid-derived tRNA were identified. We also found two short repeats that captured the nad3 and nad6 genes and resulted in two copies. In addition, nine pairs of repeat sequences were identified as being involved in the mediation of genome recombination. This is crucial for the formation of subgenomic configurations. To characterize RNA editing sites, transcriptome data were used, and we identified 480 RNA editing sites in protein-coding sequences. Among them, the initiation codon of the nad1 gene confirmed that an RNA editing event occurred, and the genomic encoded ACG was edited as AUG in the transcript. Combined with previous reports on the chloroplast genome, our data complemented our understanding of the last part of the organelle genome of plum, which will facilitate our understanding of the evolution of organelle genomes.
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Affiliation(s)
- Bo Fang
- Fruit Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (B.F.); (Q.Z.)
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China;
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, Chongqing 400716, China
| | - Qian Zhao
- Fruit Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (B.F.); (Q.Z.)
| | - Yuping Liang
- College of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China;
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China;
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, Chongqing 400716, China
- Correspondence:
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Huo H, Chen X, Guo X, Vitter JS. Efficient Compression and Indexing for Highly Repetitive DNA Sequence Collections. IEEE/ACM Trans Comput Biol Bioinform 2021; 18:2394-2408. [PMID: 31985436 DOI: 10.1109/tcbb.2020.2968323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this paper, we focus upon the important problem of indexing and searching highly repetitive DNA sequence collections. Given a collection G of t sequences Si of length n each, we can represent G succinctly in 2nHk(T) + O(n' loglogn) + o(q n') + o(tn) bits using O(t n2 + q n') time, where Hk(T) is the kth-order empirical entropy of the sequence T ∈ G that is used as the reference sequence, n' is the total number of variations between T and the sequences in G, and q is a small fixed constant. We can restore any length len substring S[ sp, ..., sp + len-1] of S ∈ G in O(ns' + len(logn)2 / loglogn) time and report all positions where P occurs in G in O(m ·t + occ ·t ·(logn)2/loglogn ) time. In addition, we propose a dynamic programming method to find the variations between T and the sequences in G in a space-efficient way, with which we can build succinct structures to enable efficient search. For highly repetitive sequences, experimental results on the tested data demonstrate that the proposed method has significant advantages in space usage and retrieval time over the current state-of-the-art methods. The source code is available online.
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Zykova T, Maltseva M, Goncharov F, Boldyreva L, Pokholkova G, Kolesnikova T, Zhimulev I. The Organization of Pericentromeric Heterochromatin in Polytene Chromosome 3 of the Drosophilamelanogaster Line with the Rif11; SuURES Su(var)3-906 Mutations Suppressing Underreplication. Cells 2021; 10:2809. [PMID: 34831030 PMCID: PMC8616060 DOI: 10.3390/cells10112809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
Although heterochromatin makes up 40% of the Drosophila melanogaster genome, its organization remains little explored, especially in polytene chromosomes, as it is virtually not represented in them due to underreplication. Two all-new approaches were used in this work: (i) with the use of a newly synthesized Drosophila line that carries three mutations, Rif11, SuURES and Su(var)3-906, suppressing the underreplication of heterochromatic regions, we obtained their fullest representation in polytene chromosomes and described their structure; (ii) 20 DNA fragments with known positions on the physical map as well as molecular genetic features of the genome (gene density, histone marks, heterochromatin proteins, origin recognition complex proteins, replication timing sites and satellite DNAs) were mapped in the newly polytenized heterochromatin using FISH and bioinformatics data. The borders of the heterochromatic regions and variations in their positions on arm 3L have been determined for the first time. The newly polytenized heterochromatic material exhibits two main types of morphology: a banding pattern (locations of genes and short satellites) and reticular chromatin (locations of large blocks of satellite DNA). The locations of the banding and reticular polytene heterochromatin was determined on the physical map.
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Affiliation(s)
- Tatyana Zykova
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
| | - Mariya Maltseva
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
| | - Fedor Goncharov
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
| | - Lidia Boldyreva
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
| | - Galina Pokholkova
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
| | - Tatyana Kolesnikova
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
- Laboratory of Structural, Functional and Comparative Genomics Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Igor Zhimulev
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
- Laboratory of Structural, Functional and Comparative Genomics Novosibirsk State University, 630090 Novosibirsk, Russia
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Subirana JA, Messeguer X. DNA Satellites Are Transcribed as Part of the Non-Coding Genome in Eukaryotes and Bacteria. Genes (Basel) 2021; 12:genes12111651. [PMID: 34828257 PMCID: PMC8625621 DOI: 10.3390/genes12111651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/16/2021] [Accepted: 10/17/2021] [Indexed: 12/01/2022] Open
Abstract
It has been shown in recent years that many repeated sequences in the genome are expressed as RNA transcripts, although the role of such RNAs is poorly understood. Some isolated and tandem repeats (satellites) have been found to be transcribed, such as mammalian Alu sequences and telomeric/centromeric satellites in different species. However, there is no detailed study on the eventual transcription of the interspersed satellites found in many species. Therefore, we decided to study for the first time the transcription of the abundant DNA satellites in the bacterium Bacillus coagulans and in the nematode Caenorhabditis elegans. We have updated the data for C. elegans satellites using the latest version of the genome. We analyzed the transcription of satellites in both species in available RNA-seq results and found that they are widely transcribed. Our demonstration that satellite RNAs are transcribed adds a new family of non-coding RNAs. This is a field that requires further investigation and will provide a deeper understanding of gene expression and control.
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Liao X, Li M, Hu K, Wu FX, Gao X, Wang J. A sensitive repeat identification framework based on short and long reads. Nucleic Acids Res 2021; 49:e100. [PMID: 34214175 PMCID: PMC8464074 DOI: 10.1093/nar/gkab563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous studies have shown that repetitive regions in genomes play indispensable roles in the evolution, inheritance and variation of living organisms. However, most existing methods cannot achieve satisfactory performance on identifying repeats in terms of both accuracy and size, since NGS reads are too short to identify long repeats whereas SMS (Single Molecule Sequencing) long reads are with high error rates. In this study, we present a novel identification framework, LongRepMarker, based on the global de novo assembly and k-mer based multiple sequence alignment for precisely marking long repeats in genomes. The major characteristics of LongRepMarker are as follows: (i) by introducing barcode linked reads and SMS long reads to assist the assembly of all short paired-end reads, it can identify the repeats to a greater extent; (ii) by finding the overlap sequences between assemblies or chomosomes, it locates the repeats faster and more accurately; (iii) by using the multi-alignment unique k-mers rather than the high frequency k-mers to identify repeats in overlap sequences, it can obtain the repeats more comprehensively and stably; (iv) by applying the parallel alignment model based on the multi-alignment unique k-mers, the efficiency of data processing can be greatly optimized and (v) by taking the corresponding identification strategies, structural variations that occur between repeats can be identified. Comprehensive experimental results show that LongRepMarker can achieve more satisfactory results than the existing de novo detection methods (https://github.com/BioinformaticsCSU/LongRepMarker).
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Affiliation(s)
- Xingyu Liao
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Min Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Kang Hu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Fang-Xiang Wu
- Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N5A9, Canada
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
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Wu S, Chen J, Li Y, Liu A, Li A, Yin M, Shrestha N, Liu J, Ren G. Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives. BMC Plant Biol 2021; 21:421. [PMID: 34521343 PMCID: PMC8438982 DOI: 10.1186/s12870-021-03202-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/31/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Although plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC. RESULTS We detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences. CONCLUSIONS Our results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes.
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Affiliation(s)
- Shuang Wu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jinyuan Chen
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ai Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ao Li
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education &State Key Lab of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.
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Chumová Z, Záveská E, Hloušková P, Ponert J, Schmidt PA, Čertner M, Mandáková T, Trávníček P. Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids. Plant J 2021; 107:511-524. [PMID: 33960537 DOI: 10.1111/tpj.15306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 05/21/2023]
Abstract
Although the evolutionary drivers of genome size change are known, the general patterns and mechanisms of plant genome size evolution are yet to be established. Here we aim to assess the relative importance of proliferation of repetitive DNA, chromosomal variation (including polyploidy), and the type of endoreplication for genome size evolution of the Pleurothallidinae, the most species-rich orchid lineage. Phylogenetic relationships between 341 Pleurothallidinae representatives were refined using a target enrichment hybrid capture combined with high-throughput sequencing approach. Genome size and the type of endoreplication were assessed using flow cytometry supplemented with karyological analysis and low-coverage Illumina sequencing for repeatome analysis on a subset of samples. Data were analyzed using phylogeny-based models. Genome size diversity (0.2-5.1 Gbp) was mostly independent of profound chromosome count variation (2n = 12-90) but tightly linked with the overall content of repetitive DNA elements. Species with partial endoreplication (PE) had significantly greater genome sizes, and genomic repeat content was tightly correlated with the size of the non-endoreplicated part of the genome. In PE species, repetitive DNA is preferentially accumulated in the non-endoreplicated parts of their genomes. Our results demonstrate that proliferation of repetitive DNA elements and PE together shape the patterns of genome size diversity in orchids.
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Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12800, Czech Republic
| | - Eliška Záveská
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, University of Innsbruck, Sternwartestraße 15, Innsbruck, 6020, Austria
| | | | - Jan Ponert
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Prague Botanical Garden, Trojská 800/196, Prague, CZ-17100, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, CZ-12844, Czech Republic
| | - Philipp-André Schmidt
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Martin Čertner
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12800, Czech Republic
| | - Terezie Mandáková
- CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
- Faculty of Science, Masaryk University, Brno, CZ-62500, Czech Republic
| | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
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Liao X, Li M, Luo J, Zou Y, Wu FX, Luo F, Wang J. EPGA-SC : A Framework for de novo Assembly of Single-Cell Sequencing Reads. IEEE/ACM Trans Comput Biol Bioinform 2021; 18:1492-1503. [PMID: 31603794 DOI: 10.1109/tcbb.2019.2945761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Assembling genomes from single-cell sequencing data is essential for single-cell studies. However, single-cell assemblies are challenging due to (i) the highly non-uniform read coverage and (ii) the elevated levels of sequencing errors and chimeric reads. Although several assemblers for single-cell data have been proposed in recent years, most of them fail to construct correct long contigs. In this study, we present a new framework called EPGA-SC for de novo assembly of single-cell sequencing reads. The EPGA assembler has designed strategies to solve the problems caused by sequencing errors, sequencing biases, and repetitive regions. However, the extremely unbalanced and richer error types prevent EPGA to achieve high performance in single-cell sequencing data. In this study, we designed EPGA-SC based on EPGA. The main innovations of EPGA-SC are as follows: (i) classifying reads to reduce the proportion of false reads; (ii) using multiple sets of high precision paired-end reads generated from the high precision assemblies produced by other assembler such as SPAdes to overcome the impact of sequencing biases and repetitive regions; and (iii) developing novel algorithms for removing chimeric errors and extending contigs. We test EPGA-SC with seven datasets. The experimental results show that EPGA-SC can generate better assemblies than most current tools in most time in term of MAX contig, N50, NG50, NA50, and NGA50.
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Liu G, Zhang T. Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation. Int J Mol Sci 2021; 22:ijms22137124. [PMID: 34281175 PMCID: PMC8268824 DOI: 10.3390/ijms22137124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
Oligonucleotides fluorescence in situ hybridization (Oligo-FISH) is an emerging technology and is an important tool in research areas such as detection of chromosome variation, identification of allopolyploid, and deciphering of three-dimensional (3D) genome structures. Based on the demand for highly efficient oligo probes for oligo-FISH experiments, increasing numbers of tools have been developed for probe design in recent years. Obsolete oligonucleotide design tools have been adapted for oligo-FISH probe design because of their similar considerations. With the development of DNA sequencing and large-scale synthesis, novel tools have been designed to increase the specificity of designed oligo probes and enable genome-scale oligo probe design, which has greatly improved the application of single copy oligo-FISH. Despite this, few studies have introduced the development of the oligo-FISH probe design tools and their application in FISH experiments systematically. Besides, a comprehensive comparison and evaluation is lacking for the available tools. In this review, we provide an overview of the oligo-FISH probe design process, summarize the development and application of the available tools, evaluate several state-of-art tools, and eventually provide guidance for single copy oligo-FISH probe design.
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Affiliation(s)
- Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Institutes of Agricultural Science and Technology Development, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Chak STC, Harris SE, Hultgren KM, Jeffery NW, Rubenstein DR. Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements. Proc Natl Acad Sci U S A 2021; 118:e2025051118. [PMID: 34099551 PMCID: PMC8214670 DOI: 10.1073/pnas.2025051118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite progress uncovering the genomic underpinnings of sociality, much less is known about how social living affects the genome. In different insect lineages, for example, eusocial species show both positive and negative associations between genome size and structure, highlighting the dynamic nature of the genome. Here, we explore the relationship between sociality and genome architecture in Synalpheus snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size. Our goal is to determine whether eusociality leads to an accumulation of repetitive elements and an increase in genome size, presumably due to reduced effective population sizes resulting from a reproductive division of labor, or whether an initial accumulation of repetitive elements leads to larger genomes and independently promotes the evolution of eusociality through adaptive evolution. Using phylogenetically informed analyses, we find that eusocial species have larger genomes with more transposable elements (TEs) and microsatellite repeats than noneusocial species. Interestingly, different TE subclasses contribute to the accumulation in different species. Phylogenetic path analysis testing alternative causal relationships between sociality and genome architecture is most consistent with the hypothesis that TEs modulate the relationship between sociality and genome architecture. Although eusociality appears to influence TE accumulation, ancestral state reconstruction suggests moderate TE abundances in ancestral species could have fueled the initial transitions to eusociality. Ultimately, we highlight a complex and dynamic relationship between genome and social evolution, demonstrating that sociality can influence the evolution of the genome, likely through changes in demography related to patterns of reproductive skew.
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Affiliation(s)
- Solomon T C Chak
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027;
- Department of Biological Sciences, State University of New York College at Old Westbury, Old Westbury, NY 11568
| | - Stephen E Harris
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
- Department of Biology, State University of New York Purchase College, Purchase, NY 10577
| | | | - Nicholas W Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS B2Y 4A2, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dustin R Rubenstein
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
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Geng Y, Liu C, Cai Q, Luo Z, Miao H, Shi X, Xu N, Fung CP, Choy TT, Yan B, Li N, Qian P, Zhou B, Zhu G. Crystal structure of parallel G-quadruplex formed by the two-repeat ALS- and FTD-related GGGGCC sequence. Nucleic Acids Res 2021; 49:5881-5890. [PMID: 34048588 PMCID: PMC8191786 DOI: 10.1093/nar/gkab302] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/23/2021] [Accepted: 05/26/2021] [Indexed: 01/05/2023] Open
Abstract
The hexanucleotide repeat expansion, GGGGCC (G4C2), within the first intron of the C9orf72 gene is known to be the most common genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The G4C2 repeat expansions, either DNA or RNA, are able to form G-quadruplexes which induce toxicity leading to ALS/FTD. Herein, we report a novel crystal structure of d(G4C2)2 that self-associates to form an eight-layer parallel tetrameric G-quadruplex. Two d(G4C2)2 associate together as a parallel dimeric G-quadruplex which folds into a tetramer via 5'-to-5' arrangements. Each dimer consists of four G-tetrads connected by two CC propeller loops. Especially, the 3'-end cytosines protrude out and form C·C+•C·C+/ C·C•C·C+ quadruple base pair or C•C·C+ triple base pair stacking on the dimeric block. Our work sheds light on the G-quadruplexes adopted by d(G4C2) and yields the invaluable structural details for the development of small molecules to tackle neurodegenerative diseases, ALS and FTD.
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Affiliation(s)
- Yanyan Geng
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Changdong Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Qixu Cai
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Zhipu Luo
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Haitao Miao
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Xiao Shi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Naining Xu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Chun Po Fung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - To To Choy
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Bing Yan
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Peiyuan Qian
- Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Bo Zhou
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
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Quan C, Li Y, Liu X, Wang Y, Ping J, Lu Y, Zhou G. Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression. Genome Biol 2021; 22:159. [PMID: 34034800 PMCID: PMC8146648 DOI: 10.1186/s13059-021-02382-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/14/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little is known of adaptive introgressed SVs in Tibetans so far. RESULTS Here, we generate a comprehensive catalog of SVs in a Chinese Tibetan (n = 15) and Han (n = 10) population using nanopore sequencing technology. Among a total of 38,216 unique SVs in the catalog, 27% are sequence-resolved for the first time. We systematically assess the distribution of these SVs across repeat sequences and functional genomic regions. Through genotyping in additional 276 genomes, we identify 69 Tibetan-Han stratified SVs and 80 candidate adaptive genes. We also discover a few adaptive introgressed SV candidates and provide evidence for a deletion of 335 base pairs at 1p36.32. CONCLUSIONS Overall, our results highlight the important role of SVs in the evolutionary processes of Tibetans' adaptation to the Qinghai-Tibet Plateau and provide a valuable resource for future high-altitude adaptation studies.
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Affiliation(s)
- Cheng Quan
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
| | - Yuanfeng Li
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
| | - Xinyi Liu
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
| | - Yahui Wang
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
| | - Jie Ping
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
| | - Yiming Lu
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
- Hebei University, Baoding, Hebei Province 071002 People’s Republic of China
| | - Gangqiao Zhou
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
- Hebei University, Baoding, Hebei Province 071002 People’s Republic of China
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province 211166 People’s Republic of China
- Medical College of Guizhou University, Guiyang, Guizhou Province 550025 People’s Republic of China
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Nguyen AH, Bachtrog D. Toxic Y chromosome: Increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome. PLoS Genet 2021; 17:e1009438. [PMID: 33886541 PMCID: PMC8061872 DOI: 10.1371/journal.pgen.1009438] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
Sex-specific differences in lifespan are prevalent across the tree of life and influenced by heteromorphic sex chromosomes. In species with XY sex chromosomes, females often outlive males. Males and females can differ in their overall repeat content due to the repetitive Y chromosome, and repeats on the Y might lower survival of the heterogametic sex (toxic Y effect). Here, we take advantage of the well-assembled young Y chromosome of Drosophila miranda to study the sex-specific dynamics of chromatin structure and repeat expression during aging in male and female flies. Male D. miranda have about twice as much repetitive DNA compared to females, and live shorter than females. Heterochromatin is crucial for silencing of repetitive elements, yet old D. miranda flies lose H3K9me3 modifications in their pericentromere, with heterochromatin loss being more severe during aging in males than females. Satellite DNA becomes de-repressed more rapidly in old vs. young male flies relative to females. In contrast to what is observed in D. melanogaster, we find that transposable elements (TEs) are expressed at higher levels in male D. miranda throughout their life. We show that epigenetic silencing via heterochromatin formation is ineffective on the TE-rich neo-Y chromosome, presumably due to active transcription of a large number of neo-Y linked genes, resulting in up-regulation of Y-linked TEs already in young males. This is consistent with an interaction between the evolutionary age of the Y chromosome and the genomic effects of aging. Our data support growing evidence that “toxic Y chromosomes” can diminish male fitness and a reduction in heterochromatin can contribute to sex-specific aging. Y chromosomes can be toxic. The Y chromosome of many species contains a large number of transposable elements (TEs), which are transcriptionally constrained by repressive chromatin marks. When relieved of these epigenetic modifications, many TEs can readily move from one genomic location to another. We show that TEs located on the Y chromosome are less effectively silenced in male Drosophila, and the toxic Y effect appears more pronounced in a species that contains a larger Y chromosome with more repeats and more actively transcribed genes. Our data demonstrate that repeat-rich Y chromosomes are a genomic liability for males.
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Affiliation(s)
- Alison H. Nguyen
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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Mendez-Dorantes C, Tsai LJ, Jahanshir E, Lopezcolorado FW, Stark JM. BLM has Contrary Effects on Repeat-Mediated Deletions, based on the Distance of DNA DSBs to a Repeat and Repeat Divergence. Cell Rep 2021; 30:1342-1357.e4. [PMID: 32023454 PMCID: PMC7085117 DOI: 10.1016/j.celrep.2020.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/08/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022] Open
Abstract
Repeat-mediated deletions (RMDs) often involve repetitive elements (e.g., short interspersed elements) with sequence divergence that is separated by several kilobase pairs (kbps). We have examined RMDs induced by DNA double-strand breaks (DSBs) under varying conditions of repeat sequence divergence (identical versus 1% and 3% divergent) and DSB/repeat distance (16 bp–28.4 kbp). We find that the BLM helicase promotes RMDs with long DSB/repeat distances (e.g., 28.4 kbp), which is consistent with a role in extensive DSB end resection, because the resection nucleases EXO1 and DNA2 affect RMDs similarly to BLM. In contrast, BLM suppresses RMDs with sequence divergence and intermediate (e.g., 3.3 kbp) DSB/repeat distances, which supports a role in heteroduplex rejection. The role of BLM in heteroduplex rejection is not epistatic with MSH2 and is independent of the annealing factor RAD52. Accordingly, the role of BLM on RMDs is substantially affected by DSB/repeat distance and repeat sequence divergence. Mendez-Dorantes et al. identify the BLM helicase as a key regulator of repeat-mediated deletions (RMDs). BLM, EXO1, and DNA2 mediate RMDs with remarkably long DNA break/repeat distances. BLM suppresses RMDs with sequence divergence that is optimal with a long non-homologous tail and is independent of MSH2 and RAD52.
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Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - L Jillianne Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Eva Jahanshir
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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Huang YS, Lu KC, Chao HW, Chen A, Chao TK, Guo CY, Hsieh HY, Shih HM, Sytwu HK, Wu CC. The MTNR1A mRNA is stabilized by the cytoplasmic hnRNPL in renal tubular cells. J Cell Physiol 2021; 236:2023-2035. [PMID: 32730662 DOI: 10.1002/jcp.29988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 12/22/2022]
Abstract
The downregulation of melatonin receptor 1A (MTNR1A) is associated with a range of pathological conditions, including membranous nephropathy. Knowledge of the mechanism underlying MTNR1A expression has been limited to the transcriptional regulation level. Here, RNA interference screening in human kidney cells revealed that heterogeneous nuclear ribonucleoprotein L (hnRNPL) upregulated MTNR1A RNA post-transcriptionally. hnRNPL knockdown or overexpression led to increased or decreased levels of cyclic adenosine monophosphate-responsive element-binding protein phosphorylation, respectively. Molecular studies showed that cytoplasmic hnRNPL exerts a stabilizing effect on the MTNR1A transcript through CA-repeat elements in its coding region. Further studies revealed that the interaction between hnRNPL and MTNR1A serves to protect MNTR1A RNA degradation by the exosome component 10 protein. MTNR1A, but not hnRNPL, displays a diurnal rhythm in mouse kidneys. Enhanced levels of MTNR1A recorded at midnight correlated with robust binding activity between cytoplasmic hnRNPL and the MTNR1A transcript. Both hnRNPL and MTNR1A were decreased in the cytoplasm of tubular epithelial cells from experimental membranous nephropathy kidneys, supporting their clinical relevance. Collectively, our data identified cytoplasmic hnRNPL as a novel player in the upregulation of MTNR1A expression in renal tubular epithelial cells, and as a potential therapeutic target.
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MESH Headings
- Animals
- Cell Line
- Circadian Rhythm/genetics
- Cyclic AMP Response Element-Binding Protein/metabolism
- Cytoplasm/metabolism
- Epithelial Cells/metabolism
- Exoribonucleases/metabolism
- Exosome Multienzyme Ribonuclease Complex/metabolism
- Glomerulonephritis, Membranous/genetics
- Glomerulonephritis, Membranous/pathology
- Heterogeneous-Nuclear Ribonucleoprotein L/metabolism
- Humans
- Kidney Tubules/metabolism
- Kidney Tubules/pathology
- Mice, Inbred BALB C
- Models, Biological
- Open Reading Frames/genetics
- Phosphorylation
- RNA Stability/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptor, Melatonin, MT1/genetics
- Receptor, Melatonin, MT1/metabolism
- Repetitive Sequences, Nucleic Acid/genetics
- Up-Regulation/genetics
- Mice
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Affiliation(s)
- Yen-Sung Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - Hsu-Wen Chao
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ann Chen
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Tai-Kuang Chao
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Yi Guo
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hsin-Yi Hsieh
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hsiu-Ming Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Huey-Kang Sytwu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Chia-Chao Wu
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
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Cabral-de-Mello DC, Marec F. Universal fluorescence in situ hybridization (FISH) protocol for mapping repetitive DNAs in insects and other arthropods. Mol Genet Genomics 2021; 296:513-526. [PMID: 33625598 DOI: 10.1007/s00438-021-01765-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/29/2021] [Indexed: 12/30/2022]
Abstract
Repetitive DNAs comprise large portion of eukaryote genomes. In genome projects, the assembly of repetitive DNAs is challenging due to the similarity between repeats, which generate ambiguities for alignment. Fluorescence in situ hybridization (FISH) is a powerful technique for the physical mapping of various sequences on chromosomes. This technique is thus very helpful in chromosome-based genome assemblies, providing information on the fine architecture of genomes and their evolution. However, various protocols are currently used for FISH mapping, most of which are relatively laborious and expensive, or work properly only with a specific type of probes or sequences, and there is a need for a universal and affordable FISH protocol. Here we tested a FISH protocol for mapping of different DNA repeats, such as multigene families (rDNAs, U snDNAs, histone genes), satellite DNAs, microsatellites, transposable elements, DOP-PCR products, and telomeric motif (TTAGG)n, on the chromosomes of various insects and other arthropods. Different cell types and stages obtained from diverse tissues were used. The FISH procedure proved high quality and reliable results in all experiments performed. We obtained data on the chromosomal distribution of DNA repeats in representatives of insects and other arthropods. Thus, our results allow us to conclude that the protocol is universal and requires only time adjustment for chromosome/DNA denaturation. The use of this FISH protocol will facilitate studies focused on understanding the evolution and role of repetitive DNA in arthropod genomes.
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Affiliation(s)
- Diogo Cavalcanti Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP- Universidade Estadual Paulista, Rio Claro, São Paulo, CEP 13506-900, Brazil.
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic.
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
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Fu L, Wang Q, Li L, Lang T, Guo J, Wang S, Sun Z, Han S, Huang B, Dong W, Zhang X, Du P. Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut. BMC Plant Biol 2021; 21:107. [PMID: 33610178 PMCID: PMC7896385 DOI: 10.1186/s12870-021-02875-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. RESULTS A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. CONCLUSIONS The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.
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Affiliation(s)
- Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Qian Wang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Lina Li
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Tao Lang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Junjia Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Siyu Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Ziqi Sun
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Suoyi Han
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Bingyan Huang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Wenzhao Dong
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Xinyou Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China.
| | - Pei Du
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China.
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Abstract
Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called 'genetic background', being able to at least potentially influence disease susceptibilities. Here, the known 'bad boys' among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany
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45
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Alamro H, Alzamel M, Iliopoulos CS, Pissis SP, Watts S. IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences. BMC Bioinformatics 2021; 22:51. [PMID: 33549041 PMCID: PMC7866733 DOI: 10.1186/s12859-021-03983-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have been linked with countless possible functions. Many international consortia provide a comprehensive description of common genetic variation making alternative sequence representations, such as IUPAC encoding, necessary for leveraging the full potential of such broad variation datasets. RESULTS We present IUPACPAL, an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats. CONCLUSION Within the parameters that were tested, our experimental results show that IUPACPAL compares favourably to a similar application packaged with EMBOSS. We show that IUPACPAL identifies many previously unidentified inverted repeats when compared with EMBOSS, and that this is also performed with orders of magnitude improved speed.
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Affiliation(s)
- Hayam Alamro
- Department of Informatics, King’s College London, 30 Aldwych, London, UK
- Department of Information Systems, Princess Nourah bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia
| | - Mai Alzamel
- Department of Informatics, King’s College London, 30 Aldwych, London, UK
- Computer Science Department, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | | | - Solon P. Pissis
- Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
- Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Steven Watts
- Department of Informatics, King’s College London, 30 Aldwych, London, UK
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46
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Abid HZ, Young E, McCaffrey J, Raseley K, Varapula D, Wang HY, Piazza D, Mell J, Xiao M. Customized optical mapping by CRISPR-Cas9 mediated DNA labeling with multiple sgRNAs. Nucleic Acids Res 2021; 49:e8. [PMID: 33231685 PMCID: PMC7826249 DOI: 10.1093/nar/gkaa1088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/16/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
Whole-genome mapping technologies have been developed as a complementary tool to provide scaffolds for genome assembly and structural variation analysis (1,2). We recently introduced a novel DNA labeling strategy based on a CRISPR-Cas9 genome editing system, which can target any 20bp sequences. The labeling strategy is specifically useful in targeting repetitive sequences, and sequences not accessible to other labeling methods. In this report, we present customized mapping strategies that extend the applications of CRISPR-Cas9 DNA labeling. We first design a CRISPR-Cas9 labeling strategy to interrogate and differentiate the single allele differences in NGG protospacer adjacent motifs (PAM sequence). Combined with sequence motif labeling, we can pinpoint the single-base differences in highly conserved sequences. In the second strategy, we design mapping patterns across a genome by selecting sets of specific single-guide RNAs (sgRNAs) for labeling multiple loci of a genomic region or a whole genome. By developing and optimizing a single tube synthesis of multiple sgRNAs, we demonstrate the utility of CRISPR-Cas9 mapping with 162 sgRNAs targeting the 2Mb Haemophilus influenzae chromosome. These CRISPR-Cas9 mapping approaches could be particularly useful for applications in defining long-distance haplotypes and pinpointing the breakpoints in large structural variants in complex genomes and microbial mixtures.
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MESH Headings
- Alleles
- Base Sequence
- Benzoxazoles/analysis
- CRISPR-Cas Systems
- Chromosome Mapping/methods
- Chromosomes, Bacterial/genetics
- Computer Simulation
- Conserved Sequence/genetics
- DNA-Directed RNA Polymerases
- Drug Resistance, Bacterial/genetics
- Fluorescent Dyes/analysis
- Gene Editing/methods
- Genome, Bacterial
- Genome, Human
- Haemophilus influenzae/drug effects
- Haemophilus influenzae/genetics
- Haplotypes/genetics
- Humans
- Lab-On-A-Chip Devices
- Nalidixic Acid/pharmacology
- Novobiocin/pharmacology
- Nucleotide Motifs/genetics
- Polymorphism, Single Nucleotide
- Quinolinium Compounds/analysis
- RNA, Guide, CRISPR-Cas Systems/chemical synthesis
- RNA, Guide, CRISPR-Cas Systems/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Alignment
- Staining and Labeling/methods
- Viral Proteins
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Affiliation(s)
- Heba Z Abid
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jennifer McCaffrey
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Hung-Yi Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Danielle Piazza
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA
| | - Joshua Mell
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA
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47
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Abstract
Every class of RNA forms base-paired structures that impact biological functions. Chemical probing of RNA structure, especially with the advent of strategies such as SHAPE-MaP, vastly expands the scale and quantitative accuracy over which RNA structure can be examined. These methods have enabled large-scale structural studies of mRNAs and lncRNAs, but the length and complexity of these RNAs makes interpretation of the data challenging. We have created modules available through the open-source Integrative Genomics Viewer (IGV) for straightforward visualization of RNA structures along with complementary experimental data. Here we present detailed and stepwise strategies for exploring and visualizing complex RNA structures in IGV. Individuals can use these instructions and supplied sample data to become adept at using IGV to visualize RNA structure models in conjunction with useful allied information.
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Affiliation(s)
- Steven Busan
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA.
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48
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Ross SE, Angeloni A, Geng FS, de Mendoza A, Bogdanovic O. Developmental remodelling of non-CG methylation at satellite DNA repeats. Nucleic Acids Res 2020; 48:12675-12688. [PMID: 33271598 PMCID: PMC7736785 DOI: 10.1093/nar/gkaa1135] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022] Open
Abstract
In vertebrates, DNA methylation predominantly occurs at CG dinucleotides however, widespread non-CG methylation (mCH) has been reported in mammalian embryonic stem cells and in the brain. In mammals, mCH is found at CAC trinucleotides in the nervous system, where it is associated with transcriptional repression, and at CAG trinucleotides in embryonic stem cells, where it positively correlates with transcription. Moreover, CAC methylation appears to be a conserved feature of adult vertebrate brains. Unlike any of those methylation signatures, here we describe a novel form of mCH that occurs in the TGCT context within zebrafish mosaic satellite repeats. TGCT methylation is inherited from both male and female gametes, remodelled during mid-blastula transition, and re-established during gastrulation in all embryonic layers. Moreover, we identify DNA methyltransferase 3ba (Dnmt3ba) as the primary enzyme responsible for the deposition of this mCH mark. Finally, we observe that TGCT-methylated repeats are specifically associated with H3K9me3-marked heterochromatin suggestive of a functional interplay between these two gene-regulatory marks. Altogether, this work provides insight into a novel form of vertebrate mCH and highlights the substrate diversity of vertebrate DNA methyltransferases.
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Affiliation(s)
- Samuel E Ross
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Allegra Angeloni
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Fan-Suo Geng
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Alex de Mendoza
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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49
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Cross I, García E, Rodríguez ME, Arias-Pérez A, Portela-Bens S, Merlo MA, Rebordinos L. The genomic structure of the highly-conserved dmrt1 gene in Solea senegalensis (Kaup, 1868) shows an unexpected intragenic duplication. PLoS One 2020; 15:e0241518. [PMID: 33137109 PMCID: PMC7605655 DOI: 10.1371/journal.pone.0241518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/15/2020] [Indexed: 01/17/2023] Open
Abstract
Knowing the factors responsible for sex determination in a species has significant theoretical and practical implications; the dmrt1 gene (Doublesex and Mab-3 (DM)-related Transcription factor 1) plays this role in diverse animal species. Solea senegalensis is a commercially important flat fish in which females grow 30% faster than males. It has 2n = 42 chromosomes and an XX / XY chromosome system for sex determination, without heteromorph chromosomes but with sex proto-chromosome. In the present study, we are providing the genomic structure and nucleotide sequence of dmrt1 gene obtained from cDNA from male and female adult gonads. A cDNA of 2027 containing an open-reading frame (ORF) of 1206 bp and encoding a 402 aa protein it is described for dmrt1 gene of S. senegalensis. Multiple mRNA isoforms indicating a high variable system of alternative splicing in the expression of dmrt1 of the sole in gonads were studied. None isoforms could be related to sex of individuals. The genomic structure of the dmrt1 of S. senegalensis showed a gene of 31400 bp composed of 7 exons and 6 introns. It contains an unexpected duplication of more than 10399 bp, involving part of the exon I, exons II and III and a SINE element found in the sequence that it is proposed as responsible for the duplication. A mature miRNA of 21 bp in length was localized at 336 bp from exon V. Protein-protein interacting networks of the dmrt1 gene showed matches with dmrt1 protein from Cynoglossus semilaevis and a protein interaction network with 11 nodes (dmrt1 plus 10 other proteins). The phylogenetic relationship of the dmrt1 gene in S. senegalensis is consistent with the evolutionary position of its species. The molecular characterization of this gene will enhance its functional analysis and the understanding of sex differentiation in Solea senegalensis and other flatfish.
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Affiliation(s)
- Ismael Cross
- Area de Genética, CASEM, Universidad de Cádiz, Puerto Real, Cádiz, Spain
| | - Emilio García
- Area de Genética, CASEM, Universidad de Cádiz, Puerto Real, Cádiz, Spain
| | - María E. Rodríguez
- Area de Genética, CASEM, Universidad de Cádiz, Puerto Real, Cádiz, Spain
| | | | | | - Manuel A. Merlo
- Area de Genética, CASEM, Universidad de Cádiz, Puerto Real, Cádiz, Spain
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50
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Novák P, Guignard MS, Neumann P, Kelly LJ, Mlinarec J, Koblížková A, Dodsworth S, Kovařík A, Pellicer J, Wang W, Macas J, Leitch IJ, Leitch AR. Repeat-sequence turnover shifts fundamentally in species with large genomes. Nat Plants 2020; 6:1325-1329. [PMID: 33077876 DOI: 10.1038/s41477-020-00785-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 09/14/2020] [Indexed: 05/04/2023]
Abstract
Given the 2,400-fold range of genome sizes (0.06-148.9 Gbp (gigabase pair)) of seed plants (angiosperms and gymnosperms) with a broadly similar gene content (amounting to approximately 0.03 Gbp), the repeat-sequence content of the genome might be expected to increase with genome size, resulting in the largest genomes consisting almost entirely of repetitive sequences. Here we test this prediction, using the same bioinformatic approach for 101 species to ensure consistency in what constitutes a repeat. We reveal a fundamental change in repeat turnover in genomes above around 10 Gbp, such that species with the largest genomes are only about 55% repetitive. Given that genome size influences many plant traits, habits and life strategies, this fundamental shift in repeat dynamics is likely to affect the evolutionary trajectory of species lineages.
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Affiliation(s)
- Petr Novák
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Maïté S Guignard
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Laura J Kelly
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Jelena Mlinarec
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Steven Dodsworth
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Life Sciences, University of Bedfordshire, Luton, UK
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Wencai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK.
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
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