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Bechara ST, Kabbani LES, Maurer-Alcalá XX, Nowacki M. Identification of novel, functional, long noncoding RNAs involved in programmed, large-scale genome rearrangements. RNA (NEW YORK, N.Y.) 2022; 28:1110-1127. [PMID: 35680167 PMCID: PMC9297840 DOI: 10.1261/rna.079134.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Noncoding RNAs (ncRNAs) make up to ∼98% percent of the transcriptome of a given organism. In recent years, one relatively new class of ncRNAs, long noncoding RNAs (lncRNAs), were shown to be more than mere by-products of gene expression and regulation. The unicellular eukaryote Paramecium tetraurelia is a member of the ciliate phylum, an extremely heterogeneous group of organisms found in most bodies of water across the globe. A hallmark of ciliate genetics is nuclear dimorphism and programmed elimination of transposons and transposon-derived DNA elements, the latter of which is essential for the maintenance of the somatic genome. Paramecium and ciliates in general harbor a plethora of different ncRNA species, some of which drive the process of large-scale genome rearrangements, including DNA elimination, during sexual development. Here, we identify and validate the first known functional lncRNAs in ciliates to date. Using deep-sequencing and subsequent bioinformatic processing and experimental validation, we show that Paramecium expresses at least 15 lncRNAs. These candidates were predicted by a highly conservative pipeline, and informatic analyses hint at differential expression during development. Depletion of two lncRNAs, lnc1 and lnc15, resulted in clear phenotypes, decreased survival, morphological impairment, and a global effect on DNA elimination.
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Affiliation(s)
- Sebastian T Bechara
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Lyna E S Kabbani
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Xyrus X Maurer-Alcalá
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
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Lindblad KA, Pathmanathan JS, Moreira S, Bracht JR, Sebra RP, Hutton ER, Landweber LF. Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms. BMC Genomics 2019; 20:1037. [PMID: 31888453 PMCID: PMC6937825 DOI: 10.1186/s12864-019-6189-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/15/2019] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Whole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available. Nevertheless, assembly of short reads remains difficult, resulting in fragmented genome sequences. Ultimately, only a sequencing technology capable of capturing complete chromosomes in a single run could resolve all ambiguities. Even "third generation" sequencing technologies produce reads far shorter than most eukaryotic chromosomes. However, the ciliate Oxytricha trifallax has a somatic genome with thousands of chromosomes averaging only 3.2 kbp, making it an ideal candidate for exploring the benefits of sequencing whole chromosomes without assembly. RESULTS We used single-molecule real-time sequencing to capture thousands of complete chromosomes in single reads and to update the published Oxytricha trifallax JRB310 genome assembly. In this version, over 50% of the completed chromosomes with two telomeres derive from single reads. The improved assembly includes over 12,000 new chromosome isoforms, and demonstrates that somatic chromosomes derive from variable rearrangements between somatic segments encoded up to 191,000 base pairs away. However, while long reads reduce the need for assembly, a hybrid approach that supplements long-read sequencing with short reads for error correction produced the most complete and accurate assembly, overall. CONCLUSIONS This assembly provides the first example of complete eukaryotic chromosomes captured by single sequencing reads and demonstrates that traditional approaches to genome assembly can mask considerable structural variation.
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Affiliation(s)
- Kelsi A. Lindblad
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA
| | - Jananan S. Pathmanathan
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
| | - Sandrine Moreira
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
| | - John R. Bracht
- Department of Biology, American University, 4400 Massachusetts Avenue, NW, Washington, DC 20016 USA
| | - Robert P. Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Elizabeth R. Hutton
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA
- Watson School of Biological Sciences, One Bungtown Road, Cold Spring Harbor,, NY 11724 USA
| | - Laura F. Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
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3
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Bhat VD, McCann KL, Wang Y, Fonseca DR, Shukla T, Alexander JC, Qiu C, Wickens M, Lo TW, Tanaka Hall TM, Campbell ZT. Engineering a conserved RNA regulatory protein repurposes its biological function in vivo. eLife 2019; 8:43788. [PMID: 30652968 PMCID: PMC6351103 DOI: 10.7554/elife.43788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/15/2019] [Indexed: 12/18/2022] Open
Abstract
PUF (PUmilio/FBF) RNA-binding proteins recognize distinct elements. In C. elegans, PUF-8 binds to an 8-nt motif and restricts proliferation in the germline. Conversely, FBF-2 recognizes a 9-nt element and promotes mitosis. To understand how motif divergence relates to biological function, we first determined a crystal structure of PUF-8. Comparison of this structure to that of FBF-2 revealed a major difference in a central repeat. We devised a modified yeast 3-hybrid screen to identify mutations that confer recognition of an 8-nt element to FBF-2. We identified several such mutants and validated structurally and biochemically their binding to 8-nt RNA elements. Using genome engineering, we generated a mutant animal with a substitution in FBF-2 that confers preferential binding to the PUF-8 element. The mutant largely rescued overproliferation in animals that spontaneously generate tumors in the absence of puf-8. This work highlights the critical role of motif length in the specification of biological function.
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Affiliation(s)
- Vandita D Bhat
- Department of Biological Sciences, University of Texas Dallas, Richardson, United States
| | - Kathleen L McCann
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - Yeming Wang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | | | - Tarjani Shukla
- Department of Biological Sciences, University of Texas Dallas, Richardson, United States
| | | | - Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - Marv Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Te-Wen Lo
- Department of Biology, Ithaca College, Ithaca, United States
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas Dallas, Richardson, United States
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Postberg J, Jönsson F, Weil PP, Bulic A, Juranek SA, Lipps HJ. 27nt-RNAs guide histone variant deposition via 'RNA-induced DNA replication interference' and thus transmit parental genome partitioning in Stylonychia. Epigenetics Chromatin 2018; 11:31. [PMID: 29895326 PMCID: PMC5996456 DOI: 10.1186/s13072-018-0201-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/04/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During sexual reproduction in the unicellular ciliate Stylonychia somatic macronuclei differentiate from germline micronuclei. Thereby, programmed sequence reduction takes place, leading to the elimination of > 95% of germline sequences, which priorly adopt heterochromatin structure via H3K27me3. Simultaneously, 27nt-ncRNAs become synthesized from parental transcripts and are bound by the Argonaute protein PIWI1. RESULTS These 27nt-ncRNAs cover sequences destined to the developing macronucleus and are thought to protect them from degradation. We provide evidence and propose that RNA/DNA base-pairing guides PIWI1/27nt-RNA complexes to complementary macronucleus-destined DNA target sequences, hence transiently causing locally stalled replication during polytene chromosome formation. This spatiotemporal delay enables the selective deposition of temporarily available histone H3.4K27me3 nucleosomes at all other sequences being continuously replicated, thus dictating their prospective heterochromatin structure before becoming developmentally eliminated. Concomitantly, 27nt-RNA-covered sites remain protected. CONCLUSIONS We introduce the concept of 'RNA-induced DNA replication interference' and explain how the parental functional genome partition could become transmitted to the progeny.
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Affiliation(s)
- Jan Postberg
- Clinical Molecular Genetics and Epigenetics, Centre for Biomedical Education and Research (ZBAF), Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448 Witten, Germany
- HELIOS University Hospital Wuppertal, Centre for Clinical and Translational Research (CCTR), HELIOS Medical Centre Wuppertal, Witten/Herdecke University, Heusnerstr. 40, 42283 Wuppertal, Germany
| | - Franziska Jönsson
- Institute of Cell Biology, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Patrick Philipp Weil
- Clinical Molecular Genetics and Epigenetics, Centre for Biomedical Education and Research (ZBAF), Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448 Witten, Germany
- HELIOS University Hospital Wuppertal, Centre for Clinical and Translational Research (CCTR), HELIOS Medical Centre Wuppertal, Witten/Herdecke University, Heusnerstr. 40, 42283 Wuppertal, Germany
| | - Aneta Bulic
- Institute of Cell Biology, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Stefan Andreas Juranek
- iPSC CRISPR Facility, European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, Groningen, The Netherlands
| | - Hans-Joachim Lipps
- Institute of Cell Biology, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
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Michelini F, Jalihal AP, Francia S, Meers C, Neeb ZT, Rossiello F, Gioia U, Aguado J, Jones-Weinert C, Luke B, Biamonti G, Nowacki M, Storici F, Carninci P, Walter NG, d'Adda di Fagagna F. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem Rev 2018; 118:4365-4403. [PMID: 29600857 DOI: 10.1021/acs.chemrev.7b00487] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.
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Affiliation(s)
- Flavia Michelini
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Ameya P Jalihal
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Sofia Francia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Chance Meers
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Zachary T Neeb
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | | | - Ubaldo Gioia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Julio Aguado
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | | | - Brian Luke
- Institute of Developmental Biology and Neurobiology , Johannes Gutenberg University , 55099 Mainz , Germany.,Institute of Molecular Biology (IMB) , 55128 Mainz , Germany
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Mariusz Nowacki
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | - Francesca Storici
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Piero Carninci
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku , Yokohama City , Kanagawa 230-0045 , Japan
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Fabrizio d'Adda di Fagagna
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
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Neeb ZT, Nowacki M. RNA-mediated transgenerational inheritance in ciliates and plants. Chromosoma 2018; 127:19-27. [PMID: 29230532 PMCID: PMC5818585 DOI: 10.1007/s00412-017-0655-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/05/2017] [Accepted: 12/05/2017] [Indexed: 11/30/2022]
Abstract
In the age of next-generation sequencing (NGS) and with the availability of whole sequenced genomes and epigenomes, some attention has shifted from purely sequence-based studies to those of heritable epigenetic modifications. Transgenerational inheritance can be defined as heritable changes to the state of DNA that may be passed on to subsequent generations without alterations to the underlying DNA sequence. Although this phenomenon has been extensively studied in many systems, studies of transgenerational inheritance in mammals and other higher-level eukaryotes may be complicated by the fact that many epigenetic marks are reprogrammed during sexual reproduction. This, by definition, may obscure our interpretation of what is in fact truly transgenerational. Therefore, in this mini review, we discuss what is currently known in the field about transgenerational epigenetic inheritance in ciliates and plants, with a particular emphasis on RNA-mediated processes and changes in chromatin states.
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Affiliation(s)
- Zachary T Neeb
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012, Bern, Switzerland
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012, Bern, Switzerland.
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