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Sizer RE, Chahid N, Butterfield SP, Donze D, Bryant NJ, White RJ. TFIIIC-based chromatin insulators through eukaryotic evolution. Gene X 2022; 835:146533. [PMID: 35623477 DOI: 10.1016/j.gene.2022.146533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 04/19/2022] [Accepted: 04/29/2022] [Indexed: 11/04/2022] Open
Abstract
Eukaryotic chromosomes are divided into domains with distinct structural and functional properties, such as differing levels of chromatin compaction and gene transcription. Domains of relatively compact chromatin and minimal transcription are termed heterochromatic, whereas euchromatin is more open and actively transcribed. Insulators separate these domains and maintain their distinct features. Disruption of insulators can cause diseases such as cancer. Many insulators contain tRNA genes (tDNAs), examples of which have been shown to block the spread of activating or silencing activities. This characteristic of specific tDNAs is conserved through evolution, such that human tDNAs can serve as barriers to the spread of silencing in fission yeast. Here we demonstrate that tDNAs from the methylotrophic fungus Pichia pastoris can function effectively as insulators in distantly-related budding yeast. Key to the function of tDNAs as insulators is TFIIIC, a transcription factor that is also required for their expression. TFIIIC binds additional loci besides tDNAs, some of which have insulator activity. Although the mechanistic basis of TFIIIC-based insulation has been studied extensively in yeast, it is largely uncharacterized in metazoa. Utilising publicly-available genome-wide ChIP-seq data, we consider the extent to which mechanisms conserved from yeast to man may suffice to allow efficient insulation by TFIIIC in the more challenging chromatin environments of metazoa and suggest features that may have been acquired during evolution to cope with new challenges. We demonstrate the widespread presence at human tDNAs of USF1, a transcription factor with well-established barrier activity in vertebrates. We predict that tDNA-based insulators in higher organisms have evolved through incorporation of modules, such as binding sites for factors like USF1 and CTCF that are absent from yeasts, thereby strengthening function and providing opportunities for regulation between cell types.
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Affiliation(s)
- Rebecca E Sizer
- Department of Biology, The University of York, York YO10 5DD, UK
| | - Nisreen Chahid
- Department of Biology, The University of York, York YO10 5DD, UK
| | | | - David Donze
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Nia J Bryant
- Department of Biology, The University of York, York YO10 5DD, UK
| | - Robert J White
- Department of Biology, The University of York, York YO10 5DD, UK.
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2
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Raices M, D'Angelo MA. Structure, Maintenance, and Regulation of Nuclear Pore Complexes: The Gatekeepers of the Eukaryotic Genome. Cold Spring Harb Perspect Biol 2022; 14:a040691. [PMID: 34312247 PMCID: PMC8789946 DOI: 10.1101/cshperspect.a040691] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, the genetic material is segregated inside the nucleus. This compartmentalization of the genome requires a transport system that allows cells to move molecules across the nuclear envelope, the membrane-based barrier that surrounds the chromosomes. Nuclear pore complexes (NPCs) are the central component of the nuclear transport machinery. These large protein channels penetrate the nuclear envelope, creating a passage between the nucleus and the cytoplasm through which nucleocytoplasmic molecule exchange occurs. NPCs are one of the largest protein assemblies of eukaryotic cells and, in addition to their critical function in nuclear transport, these structures also play key roles in many cellular processes in a transport-independent manner. Here we will review the current knowledge of the NPC structure, the cellular mechanisms that regulate their formation and maintenance, and we will provide a brief description of a variety of processes that NPCs regulate.
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Affiliation(s)
- Marcela Raices
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
| | - Maximiliano A D'Angelo
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
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3
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de la Cruz Ruiz P, Romero-Bueno R, Askjaer P. Analysis of Nuclear Pore Complexes in Caenorhabditis elegans by Live Imaging and Functional Genomics. Methods Mol Biol 2022; 2502:161-182. [PMID: 35412238 DOI: 10.1007/978-1-0716-2337-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nuclear pore complexes (NPCs) are essential to communication of macromolecules between the cell nucleus and the surrounding cytoplasm. RNA synthesized in the nucleus is exported through NPCs to function in the cytoplasm, whereas transcription factors and other proteins are selectively and actively imported. In addition, many NPC constituents, known as nuclear pore proteins (nucleoporins or nups), also play critical roles in other processes, such as genome organization, gene expression, and kinetochore function. Thanks to its genetic amenability and transparent body, the nematode Caenorhabditis elegans is an attractive model to study NPC dynamics. We provide here an overview of available genome engineered strains and FLP/Frt-based tools to study tissue-specific functions of individual nucleoporins. We also present protocols for live imaging of fluorescently tagged nucleoporins in intact tissues of embryos, larvae, and adult and for analysis of interactions between nucleoporins and chromatin by DamID.
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Affiliation(s)
- Patricia de la Cruz Ruiz
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Raquel Romero-Bueno
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain.
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4
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Bonnet A, Chaput C, Palmic N, Palancade B, Lesage P. A nuclear pore sub-complex restricts the propagation of Ty retrotransposons by limiting their transcription. PLoS Genet 2021; 17:e1009889. [PMID: 34723966 PMCID: PMC8585004 DOI: 10.1371/journal.pgen.1009889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/11/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Beyond their canonical function in nucleocytoplasmic exchanges, nuclear pore complexes (NPCs) regulate the expression of protein-coding genes. Here, we have implemented transcriptomic and molecular methods to specifically address the impact of the NPC on retroelements, which are present in multiple copies in genomes. We report a novel function for the Nup84 complex, a core NPC building block, in specifically restricting the transcription of LTR-retrotransposons in yeast. Nup84 complex-dependent repression impacts both Copia and Gypsy Ty LTR-retrotransposons, all over the S. cerevisiae genome. Mechanistically, the Nup84 complex restricts the transcription of Ty1, the most active yeast retrotransposon, through the tethering of the SUMO-deconjugating enzyme Ulp1 to NPCs. Strikingly, the modest accumulation of Ty1 RNAs caused by Nup84 complex loss-of-function is sufficient to trigger an important increase of Ty1 cDNA levels, resulting in massive Ty1 retrotransposition. Altogether, our study expands our understanding of the complex interactions between retrotransposons and the NPC, and highlights the importance for the cells to keep retrotransposons under tight transcriptional control.
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Affiliation(s)
- Amandine Bonnet
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Carole Chaput
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Noé Palmic
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Pascale Lesage
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
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5
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Kulaberoglu Y, Malik Y, Borland G, Selman C, Alic N, Tullet JMA. RNA Polymerase III, Ageing and Longevity. Front Genet 2021; 12:705122. [PMID: 34295356 PMCID: PMC8290157 DOI: 10.3389/fgene.2021.705122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription in eukaryotic cells is performed by three RNA polymerases. RNA polymerase I synthesises most rRNAs, whilst RNA polymerase II transcribes all mRNAs and many non-coding RNAs. The largest of the three polymerases is RNA polymerase III (Pol III) which transcribes a variety of short non-coding RNAs including tRNAs and the 5S rRNA, in addition to other small RNAs such as snRNAs, snoRNAs, SINEs, 7SL RNA, Y RNA, and U6 spilceosomal RNA. Pol III-mediated transcription is highly dynamic and regulated in response to changes in cell growth, cell proliferation and stress. Pol III-generated transcripts are involved in a wide variety of cellular processes, including translation, genome and transcriptome regulation and RNA processing, with Pol III dys-regulation implicated in diseases including leukodystrophy, Alzheimer's, Fragile X-syndrome and various cancers. More recently, Pol III was identified as an evolutionarily conserved determinant of organismal lifespan acting downstream of mTORC1. Pol III inhibition extends lifespan in yeast, worms and flies, and in worms and flies acts from the intestine and intestinal stem cells respectively to achieve this. Intriguingly, Pol III activation achieved through impairment of its master repressor, Maf1, has also been shown to promote longevity in model organisms, including mice. In this review we introduce the Pol III transcription apparatus and review the current understanding of RNA Pol III's role in ageing and lifespan in different model organisms. We then discuss the potential of Pol III as a therapeutic target to improve age-related health in humans.
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Affiliation(s)
- Yavuz Kulaberoglu
- Department of Genetics Evolution and Environment, Institute of Healthy Ageing, University College London, London, United Kingdom
| | - Yasir Malik
- Faculty of Natural Sciences, University of Kent, Canterbury, United Kingdom
| | - Gillian Borland
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Colin Selman
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Nazif Alic
- Department of Genetics Evolution and Environment, Institute of Healthy Ageing, University College London, London, United Kingdom.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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6
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Jarrous N, Mani D, Ramanathan A. Coordination of transcription and processing of tRNA. FEBS J 2021; 289:3630-3641. [PMID: 33929081 DOI: 10.1111/febs.15904] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/02/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022]
Abstract
Coordination of transcription and processing of RNA is a basic principle in regulation of gene expression in eukaryotes. In the case of mRNA, coordination is primarily founded on a co-transcriptional processing mechanism by which a nascent precursor mRNA undergoes maturation via cleavage and modification by the transcription machinery. A similar mechanism controls the biosynthesis of rRNA. However, the coordination of transcription and processing of tRNA, a rather short transcript, remains unknown. Here, we present a model for high molecular weight initiation complexes of human RNA polymerase III that assemble on tRNA genes and process precursor transcripts to mature forms. These multifunctional initiation complexes may support co-transcriptional processing, such as the removal of the 5' leader of precursor tRNA by RNase P. Based on this model, maturation of tRNA is predetermined prior to transcription initiation.
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Affiliation(s)
- Nayef Jarrous
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Dhivakar Mani
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Aravind Ramanathan
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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7
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Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics 2020; 216:931-945. [PMID: 33037050 PMCID: PMC7768263 DOI: 10.1534/genetics.120.303774] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/09/2020] [Indexed: 11/23/2022] Open
Abstract
Differential gene expression across cell types underlies development and cell physiology in multicellular organisms. Caenorhabditis elegans is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates to the difficulty to obtain comprehensive tissue-specific gene transcription data, since available methods are still challenging to execute and/or require large worm populations. Here, we introduce the RNA Polymerase DamID (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit to create transcriptional footprints via methyl marks on the DNA of transcribed genes. To validate the method, we determined the polymerase footprints in whole animals, in sorted embryonic blastomeres and in different tissues from intact young adults by driving tissue-specific Dam fusion expression. We obtained meaningful transcriptional footprints in line with RNA-sequencing (RNA-seq) studies in whole animals or specific tissues. To challenge the sensitivity of RAPID and demonstrate its utility to determine novel tissue-specific transcriptional profiles, we determined the transcriptional footprints of the pair of XXX neuroendocrine cells, representing 0.2% of the somatic cell content of the animals. We identified 3901 candidate genes with putatively active transcription in XXX cells, including the few previously known markers for these cells. Using transcriptional reporters for a subset of new hits, we confirmed that the majority of them were expressed in XXX cells and identified novel XXX-specific markers. Taken together, our work establishes RAPID as a valid method for the determination of RNA polymerase footprints in specific tissues of C. elegans without the need for cell sorting or RNA tagging.
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8
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Ojha S, Malla S, Lyons SM. snoRNPs: Functions in Ribosome Biogenesis. Biomolecules 2020; 10:biom10050783. [PMID: 32443616 PMCID: PMC7277114 DOI: 10.3390/biom10050783] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/13/2020] [Indexed: 01/18/2023] Open
Abstract
Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.
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Affiliation(s)
- Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Sulochan Malla
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Shawn M. Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-358-4280
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9
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Brickner DG, Randise-Hinchliff C, Lebrun Corbin M, Liang JM, Kim S, Sump B, D'Urso A, Kim SH, Satomura A, Schmit H, Coukos R, Hwang S, Watson R, Brickner JH. The Role of Transcription Factors and Nuclear Pore Proteins in Controlling the Spatial Organization of the Yeast Genome. Dev Cell 2020; 49:936-947.e4. [PMID: 31211995 DOI: 10.1016/j.devcel.2019.05.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/18/2019] [Accepted: 05/10/2019] [Indexed: 12/15/2022]
Abstract
Loss of nuclear pore complex (NPC) proteins, transcription factors (TFs), histone modification enzymes, Mediator, and factors involved in mRNA export disrupts the physical interaction of chromosomal sites with NPCs. Conditional inactivation and ectopic tethering experiments support a direct role for the TFs Gcn4 and Nup2 in mediating interaction with the NPC but suggest an indirect role for factors involved in mRNA export or transcription. A conserved "positioning domain" within Gcn4 controls interaction with the NPC and inter-chromosomal clustering and promotes transcription of target genes. Such a function may be quite common; a comprehensive screen reveals that tethering of most yeast TFs is sufficient to promote targeting to the NPC. While some TFs require Nup100, others do not, suggesting two distinct targeting mechanisms. These results highlight an important and underappreciated function of TFs in controlling the spatial organization of the yeast genome through interaction with the NPC.
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Affiliation(s)
- Donna Garvey Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | | | - Marine Lebrun Corbin
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Julie Ming Liang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Stephanie Kim
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Bethany Sump
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Agustina D'Urso
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Seo Hyun Kim
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Atsushi Satomura
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Heidi Schmit
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Robert Coukos
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Subin Hwang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Raven Watson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA.
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10
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Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans. Epigenetics Chromatin 2020; 13:1. [PMID: 31918747 PMCID: PMC6950938 DOI: 10.1186/s13072-019-0325-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/20/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromatin organization is central to precise control of gene expression. In various eukaryotic species, domains of pervasive cis-chromatin interactions demarcate functional domains of the genomes. In nematode Caenorhabditis elegans, however, pervasive chromatin contact domains are limited to the dosage-compensated sex chromosome, leaving the principle of C. elegans chromatin organization unclear. Transcription factor III C (TFIIIC) is a basal transcription factor complex for RNA polymerase III, and is implicated in chromatin organization. TFIIIC binding without RNA polymerase III co-occupancy, referred to as extra-TFIIIC binding, has been implicated in insulating active and inactive chromatin domains in yeasts, flies, and mammalian cells. Whether extra-TFIIIC sites are present and contribute to chromatin organization in C. elegans remains unknown. RESULTS We identified 504 TFIIIC-bound sites absent of RNA polymerase III and TATA-binding protein co-occupancy characteristic of extra-TFIIIC sites in C. elegans embryos. Extra-TFIIIC sites constituted half of all identified TFIIIC binding sites in the genome. Extra-TFIIIC sites formed dense clusters in cis. The clusters of extra-TFIIIC sites were highly over-represented within the distal arm domains of the autosomes that presented a high level of heterochromatin-associated histone H3K9 trimethylation (H3K9me3). Furthermore, extra-TFIIIC clusters were embedded in the lamina-associated domains. Despite the heterochromatin environment of extra-TFIIIC sites, the individual clusters of extra-TFIIIC sites were devoid of and resided near the individual H3K9me3-marked regions. CONCLUSION Clusters of extra-TFIIIC sites were pervasive in the arm domains of C. elegans autosomes, near the outer boundaries of H3K9me3-marked regions. Given the reported activity of extra-TFIIIC sites in heterochromatin insulation in yeasts, our observation raised the possibility that TFIIIC may also demarcate heterochromatin in C. elegans.
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11
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Bahin M, Noël BF, Murigneux V, Bernard C, Bastianelli L, Le Hir H, Lebreton A, Genovesio A. ALFA: annotation landscape for aligned reads. BMC Genomics 2019; 20:250. [PMID: 30922228 PMCID: PMC6440077 DOI: 10.1186/s12864-019-5624-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 03/20/2019] [Indexed: 01/14/2023] Open
Abstract
Background The last 10 years have seen the rise of countless functional genomics studies based on Next-Generation Sequencing (NGS). In the vast majority of cases, whatever the species, whatever the experiment, the two first steps of data analysis consist of a quality control of the raw reads followed by a mapping of those reads to a reference genome/transcriptome. Subsequent steps then depend on the type of study that is being made. While some tools have been proposed for investigating data quality after the mapping step, there is no commonly adopted framework that would be easy to use and broadly applicable to any NGS data type. Results We present ALFA, a simple but universal tool that can be used after the mapping step on any kind of NGS experiment data for any organism with available genomic annotations. In a single command line, ALFA can compute and display distribution of reads by categories (exon, intron, UTR, etc.) and biotypes (protein coding, miRNA, etc.) for a given aligned dataset with nucleotide precision. We present applications of ALFA to Ribo-Seq and RNA-Seq on Homo sapiens, CLIP-Seq on Mus musculus, RNA-Seq on Saccharomyces cerevisiae, Bisulfite sequencing on Arabidopsis thaliana and ChIP-Seq on Caenorhabditis elegans. Conclusions We show that ALFA provides a powerful and broadly applicable approach for post mapping quality control and to produce a global overview using common or dedicated annotations. It is made available to the community as an easy to install command line tool and from the Galaxy Tool Shed.
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Affiliation(s)
- Mathieu Bahin
- Computational Biology and Bioinformatics group,, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Benoit F Noël
- Computational Biology and Bioinformatics group,, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.,Bacterial Infection & RNA Destiny group, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Valentine Murigneux
- Expression of eukaryotic messenger RNAs group, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Charles Bernard
- Computational Biology and Bioinformatics group,, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Leila Bastianelli
- Computational Biology and Bioinformatics group,, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.,Expression of eukaryotic messenger RNAs group, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Hervé Le Hir
- Expression of eukaryotic messenger RNAs group, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Alice Lebreton
- Bacterial Infection & RNA Destiny group, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France. .,INRA, IBENS, 75005, Paris, France.
| | - Auguste Genovesio
- Computational Biology and Bioinformatics group,, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.
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12
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Robijns J, Houthaeve G, Braeckmans K, De Vos WH. Loss of Nuclear Envelope Integrity in Aging and Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 336:205-222. [DOI: 10.1016/bs.ircmb.2017.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Misale MS, Witek Janusek L, Tell D, Mathews HL. Chromatin organization as an indicator of glucocorticoid induced natural killer cell dysfunction. Brain Behav Immun 2018; 67:279-289. [PMID: 28911980 PMCID: PMC5696065 DOI: 10.1016/j.bbi.2017.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 09/01/2017] [Accepted: 09/08/2017] [Indexed: 11/19/2022] Open
Abstract
It is well-established that psychological distress reduces natural killer cell immune function and that this reduction can be due to the stress-induced release of glucocorticoids. Glucocorticoids are known to alter epigenetic marks associated with immune effector loci, and are also known to influence chromatin organization. The purpose of this investigation was to assess the effect of glucocorticoids on natural killer cell chromatin organization and to determine the relationship of chromatin organization to natural killer cell effector function, e.g. interferon gamma production. Interferon gamma production is the prototypic cytokine produced by natural killer cells and is known to modulate both innate and adaptive immunity. Glucocorticoid treatment of human peripheral blood mononuclear cells resulted in a significant reduction in interferon gamma production. Glucocorticoid treatment also resulted in a demonstrable natural killer cell nuclear phenotype. This phenotype was localization of the histone, post-translational epigenetic mark, H3K27me3, to the nuclear periphery. Peripheral nuclear localization of H3K27me3 was directly related to cellular levels of interferon gamma. This nuclear phenotype was determined by direct visual inspection and by use of an automated, high through-put technology, the Amnis ImageStream. This technology combines the per-cell information content provided by standard microscopy with the statistical significance afforded by large sample sizes common to standard flow cytometry. Most importantly, this technology provides for a direct assessment of the localization of signal intensity within individual cells. The results demonstrate glucocorticoids to dysregulate natural killer cell function at least in part through altered H3K27me3 nuclear organization and demonstrate H3K27me3 chromatin organization to be a predictive indicator of glucocorticoid induced immune dysregulation of natural killer cells.
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Affiliation(s)
- Michael S Misale
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States
| | - Linda Witek Janusek
- Marcella Niehoff School of Nursing, Department of Health Promotion, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States
| | - Dina Tell
- Marcella Niehoff School of Nursing, Department of Health Promotion, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States
| | - Herbert L Mathews
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States.
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14
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Jarrous N. Roles of RNase P and Its Subunits. Trends Genet 2017; 33:594-603. [PMID: 28697848 DOI: 10.1016/j.tig.2017.06.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/18/2017] [Accepted: 06/20/2017] [Indexed: 12/11/2022]
Abstract
Recent studies show that nuclear RNase P is linked to chromatin structure and function. Thus, variants of this ribonucleoprotein (RNP) complex bind to chromatin of small noncoding RNA genes; integrate into initiation complexes of RNA polymerase (Pol) III; repress histone H3.3 nucleosome deposition; control tRNA and PIWI-interacting RNA (piRNA) gene clusters for genome defense; and respond to Werner syndrome helicase (WRN)-related replication stress and DNA double-strand breaks (DSBs). Likewise, the related RNase MRP and RMRP-TERT (telomerase reverse transcriptase) are implicated in RNA-dependent RNA polymerization for chromatin silencing, whereas the telomerase carries out RNA-dependent DNA polymerization for telomere lengthening. Remarkably, the four RNPs share several protein subunits, including two Alba-like chromatin proteins that possess DEAD-like and ATPase motifs found in chromatin modifiers and remodelers. Based on available data, RNase P and related RNPs act in transition processes of DNA to RNA and vice versa and connect these processes to genome preservation, including replication, DNA repair, and chromatin remodeling.
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Affiliation(s)
- Nayef Jarrous
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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15
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Yuen KC, Slaughter BD, Gerton JL. Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports the expression of active dense gene clusters. SCIENCE ADVANCES 2017; 3:e1700191. [PMID: 28691095 PMCID: PMC5479651 DOI: 10.1126/sciadv.1700191] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/05/2017] [Indexed: 05/26/2023]
Abstract
Structural maintenance of chromosome complexes, such as cohesin, have been implicated in a wide variety of chromatin-dependent functions such as genome organization, replication, and gene expression. How these complexes find their sites of association and affect local chromosomal processes is not well understood. We report that condensin II, a complex distinct from cohesin, physically interacts with TFIIIC, and they both colocalize at active gene promoters in the mouse and human genomes, facilitated by interaction between NCAPD3 and the epigenetic mark H3K4me3. Condensin II is important for maintaining high levels of expression of the histone gene clusters as well as the interaction between these clusters in the mouse genome. Our findings suggest that condensin II is anchored to the mammalian genome by a combination of H3K4me3 and the sequence-specific binding of TFIIIC, and that condensin supports the expression of active gene-dense regions found at the boundaries of topological domains. Together, our results support a working model in which condensin II contributes to topological domain boundary-associated gene activity in the mammalian genome.
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Affiliation(s)
- Kobe C. Yuen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA
- University of Kansas Cancer Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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16
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Sin O, de Jong T, Mata-Cabana A, Kudron M, Zaini MA, Aprile FA, Seinstra RI, Stroo E, Prins RW, Martineau CN, Wang HH, Hogewerf W, Steinhof A, Wanker EE, Vendruscolo M, Calkhoven CF, Reinke V, Guryev V, Nollen EAA. Identification of an RNA Polymerase III Regulator Linked to Disease-Associated Protein Aggregation. Mol Cell 2017; 65:1096-1108.e6. [PMID: 28306505 PMCID: PMC5364375 DOI: 10.1016/j.molcel.2017.02.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/05/2017] [Accepted: 02/22/2017] [Indexed: 11/24/2022]
Abstract
Protein aggregation is associated with age-related neurodegenerative disorders, such as Alzheimer's and polyglutamine diseases. As a causal relationship between protein aggregation and neurodegeneration remains elusive, understanding the cellular mechanisms regulating protein aggregation will help develop future treatments. To identify such mechanisms, we conducted a forward genetic screen in a C. elegans model of polyglutamine aggregation and identified the protein MOAG-2/LIR-3 as a driver of protein aggregation. In the absence of polyglutamine, MOAG-2/LIR-3 regulates the RNA polymerase III-associated transcription of small non-coding RNAs. This regulation is lost in the presence of polyglutamine, which mislocalizes MOAG-2/LIR-3 from the nucleus to the cytosol. We then show biochemically that MOAG-2/LIR-3 can also catalyze the aggregation of polyglutamine-expanded huntingtin. These results suggest that polyglutamine can induce an aggregation-promoting activity of MOAG-2/LIR-3 in the cytosol. The concept that certain aggregation-prone proteins can convert other endogenous proteins into drivers of aggregation and toxicity adds to the understanding of how cellular homeostasis can be deteriorated in protein misfolding diseases.
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Affiliation(s)
- Olga Sin
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands; Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Tristan de Jong
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Alejandro Mata-Cabana
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Michelle Kudron
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mohamad Amr Zaini
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | | | - Renée I Seinstra
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Esther Stroo
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Roméo Willinge Prins
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Céline N Martineau
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Hai Hui Wang
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Wytse Hogewerf
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Anne Steinhof
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Erich E Wanker
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Cornelis F Calkhoven
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Valerie Reinke
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands.
| | - Ellen A A Nollen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands.
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17
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Ferreira J, Stear JH, Saumweber H. Nucleoporins NPP-10, NPP-13 and NPP-20 are required for HCP-4 nuclear import to establish correct centromere assembly. J Cell Sci 2017; 130:963-974. [PMID: 28122936 DOI: 10.1242/jcs.196709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/13/2017] [Indexed: 12/15/2022] Open
Abstract
Centromeres form a chromosomal platform for the assembly of the kinetochores, which are required for orderly chromosome segregation. Assembly of both centromeres and kinetochores proceeds by a step-by-step mechanism that is regulated in time and space. It has been suggested that the regulated nuclear import of centromeric proteins is involved in this process. We show that the knockdown of nucleoporins NPP-10, NPP-13 and NPP-20 in Caenorhabditiselegans affects early steps in centromere formation and sister centromere resolution, and results in severe chromosomal defects in the early embryo. These phenotypes mirror the knockdown phenotype of HCP-4 (an ortholog of mammalian CENP-C), a key factor for centromere formation and inner kinetochore assembly. HCP-4 is present in the cytoplasm during interphase. It is imported into nuclei and assembled in centromeres during prophase. Following the knockdown of NPP-10, NPP-13 and NPP-20, HCP-4 remains in the cytosol throughout prophase due to stalled import. In prometaphase and later mitotic stages after breakdown of the nuclear envelope, HCP-4 is not incorporated into centromeres. These results indicate that correct timing of the availability of HCP-4 by nuclear import is essential.
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Affiliation(s)
- Jorge Ferreira
- Cytogenetics group, Institute of Biology, Humboldt-Universität zu Berlin, Chausseestr. 117, Berlin 10115, Germany
| | - Jeffrey H Stear
- University of New South Wales, School of Medical Sciences, Sydney, New South Wales 2052, Australia
| | - Harald Saumweber
- Cytogenetics group, Institute of Biology, Humboldt-Universität zu Berlin, Chausseestr. 117, Berlin 10115, Germany
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18
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Raices M, D'Angelo MA. Nuclear pore complexes and regulation of gene expression. Curr Opin Cell Biol 2017; 46:26-32. [PMID: 28088069 DOI: 10.1016/j.ceb.2016.12.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/09/2016] [Accepted: 12/21/2016] [Indexed: 12/31/2022]
Abstract
Nuclear pore complexes (NPCs), are large multiprotein channels that penetrate the nuclear envelope connecting the nucleus to the cytoplasm. Accumulating evidence shows that besides their main role in regulating the exchange of molecules between these two compartments, NPCs and their components also play important transport-independent roles, including gene expression regulation, chromatin organization, DNA repair, RNA processing and quality control, and cell cycle control. Here, we will describe the recent findings about the role of these structures in the regulation of gene expression.
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Affiliation(s)
- Marcela Raices
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, 10901 N. Torrey Pines Road, La Jolla, 92037 CA, United States
| | - Maximiliano A D'Angelo
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, 10901 N. Torrey Pines Road, La Jolla, 92037 CA, United States.
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19
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Cohen-Fix O, Askjaer P. Cell Biology of the Caenorhabditis elegans Nucleus. Genetics 2017; 205:25-59. [PMID: 28049702 PMCID: PMC5216270 DOI: 10.1534/genetics.116.197160] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/09/2016] [Indexed: 12/25/2022] Open
Abstract
Studies on the Caenorhabditis elegans nucleus have provided fascinating insight to the organization and activities of eukaryotic cells. Being the organelle that holds the genetic blueprint of the cell, the nucleus is critical for basically every aspect of cell biology. The stereotypical development of C. elegans from a one cell-stage embryo to a fertile hermaphrodite with 959 somatic nuclei has allowed the identification of mutants with specific alterations in gene expression programs, nuclear morphology, or nuclear positioning. Moreover, the early C. elegans embryo is an excellent model to dissect the mitotic processes of nuclear disassembly and reformation with high spatiotemporal resolution. We review here several features of the C. elegans nucleus, including its composition, structure, and dynamics. We also discuss the spatial organization of chromatin and regulation of gene expression and how this depends on tight control of nucleocytoplasmic transport. Finally, the extensive connections of the nucleus with the cytoskeleton and their implications during development are described. Most processes of the C. elegans nucleus are evolutionarily conserved, highlighting the relevance of this powerful and versatile model organism to human biology.
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Affiliation(s)
- Orna Cohen-Fix
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Peter Askjaer
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
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20
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Domanska A, Kaminska J. Role of Rsp5 ubiquitin ligase in biogenesis of rRNA, mRNA and tRNA in yeast. RNA Biol 2016; 12:1265-74. [PMID: 26403176 DOI: 10.1080/15476286.2015.1094604] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Rsp5 ubiquitin ligase is required for ubiquitination of a wide variety of proteins involved in essential processes. Rsp5 was shown to be involved in regulation of lipid biosynthesis, intracellular trafficking of proteins, response to various stresses, and many other processes. In this article, we provide a comprehensive review of the nuclear and cytoplasmic functions of Rsp5 with a focus on biogenesis of different RNAs. We also briefly describe the participation of Rsp5 in the regulation of the RNA polymerase II complex, and its potential role in the regulation of other RNA polymerases. Moreover, we emphasize the function of Rsp5 in the coordination of the different steps of rRNA, mRNA and tRNA metabolism in the context of protein biosynthesis. Finally, we highlight the involvement of Rsp5 in controlling diverse cellular mechanisms at multiple levels and in adaptation of the cell to changing growth conditions.
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Affiliation(s)
- Anna Domanska
- a Institute of Biochemistry and Biophysics, Polish Academy of Sciences ; Warsaw , Poland
| | - Joanna Kaminska
- a Institute of Biochemistry and Biophysics, Polish Academy of Sciences ; Warsaw , Poland
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21
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Ben-Yishay R, Ashkenazy AJ, Shav-Tal Y. Dynamic Encounters of Genes and Transcripts with the Nuclear Pore. Trends Genet 2016; 32:419-431. [DOI: 10.1016/j.tig.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/20/2016] [Indexed: 01/04/2023]
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22
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Gonzalez-Sandoval A, Gasser SM. On TADs and LADs: Spatial Control Over Gene Expression. Trends Genet 2016; 32:485-495. [PMID: 27312344 DOI: 10.1016/j.tig.2016.05.004] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 01/10/2023]
Abstract
The combinatorial action of transcription factors drives cell-type-specific gene expression patterns. However, transcription factor binding and gene regulation occur in the context of chromatin, which modulates DNA accessibility. High-resolution chromatin interaction maps have defined units of chromatin that are in spatial proximity, called topologically associated domains (TADs). TADs can be further classified based on expression activity, replication timing, or the histone marks or non-histone proteins associated with them. Independently, other chromatin domains have been defined by their likelihood to interact with non-DNA structures, such as the nuclear lamina. Lamina-associated domains (LADs) correlate with low gene expression and late replication timing. TADs and LADs have recently been evaluated with respect to cell-type-specific gene expression. The results shed light on the relevance of these forms of chromatin organization for transcriptional regulation, and address specifically how chromatin sequestration influences cell fate decisions during organismal development.
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Affiliation(s)
- Adriana Gonzalez-Sandoval
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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23
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RNA Polymerase III Advances: Structural and tRNA Functional Views. Trends Biochem Sci 2016; 41:546-559. [PMID: 27068803 DOI: 10.1016/j.tibs.2016.03.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 12/25/2022]
Abstract
RNA synthesis in eukaryotes is divided among three RNA polymerases (RNAPs). RNAP III transcribes hundreds of tRNA genes and fewer additional short RNA genes. We survey recent work on transcription by RNAP III including an atomic structure, mechanisms of action, interactions with chromatin and retroposons, and a conserved link between its activity and a tRNA modification that enhances mRNA decoding. Other new work suggests important mechanistic connections to oxidative stress, autoimmunity and cancer, embryonic stem cell pluripotency, and tissue-specific developmental effects. We consider that, for some of its complex functions, variation in RNAP III activity levels lead to nonuniform changes in tRNAs that can shift the translation profiles of key codon-biased mRNAs with resultant phenotypes or disease states.
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24
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Sharma R, Meister P. Dosage compensation and nuclear organization: cluster to control chromosome-wide gene expression. Curr Opin Genet Dev 2016; 37:9-16. [PMID: 26748388 DOI: 10.1016/j.gde.2015.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 11/18/2015] [Accepted: 11/25/2015] [Indexed: 11/28/2022]
Abstract
In many species, male and female animals differ in the number of X chromosomes they possess. As a consequence, large scale differences in gene dosage exist between sexes; a phenomenon that is rarely tolerated by the organism for changes in autosome dosage. Several strategies have evolved independently to balance X-linked gene dosage between sexes, named dosage compensation (DC). The molecular basis of DC differs among the three best-studied examples: mammals, fruit fly and nematodes. In this short review, we summarize recent microscopic and chromosome conformation capture data that reveal key features of the compensated X chromosome and highlight the events leading to the establishment of a functional, specialized nuclear compartment, the X domain.
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Affiliation(s)
- Rahul Sharma
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Switzerland.
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25
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Abstract
Breuer and Ohkura propose a negative regulatory loop within the nuclear pore complex (NPC) controlling the chromatin attachment state, in which Nup155 and Nup93 recruit Nup62 to suppress chromatin tethering by Nup155. The nuclear pore complex (NPC) tethers chromatin to create an environment for gene regulation, but little is known about how this activity is regulated to avoid excessive tethering of the genome. Here we propose a negative regulatory loop within the NPC controlling the chromatin attachment state, in which Nup155 and Nup93 recruit Nup62 to suppress chromatin tethering by Nup155. Depletion of Nup62 severely disrupts chromatin distribution in the nuclei of female germlines and somatic cells, which can be reversed by codepleting Nup155. Thus, this universal regulatory system within the NPC is crucial to control large-scale chromatin organization in the nucleus.
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Affiliation(s)
- Manuel Breuer
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Hiroyuki Ohkura
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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26
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Sharma R, Meister P. Linking dosage compensation and X chromosome nuclear organization in C. elegans. Nucleus 2015; 6:266-72. [PMID: 26055265 DOI: 10.1080/19491034.2015.1059546] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Animal sex is determined by the number of X chromosomes in many species, creating unequal gene dosage (aneuploidy) between sexes. Dosage Compensation mechanisms equalize this dosage difference by regulating X-linked gene expression. In the nematode C. elegans the current model suggests that DC is achieved by a 2-fold transcriptional downregulation in hermaphrodites mediated by the Dosage Compensation Complex (DCC), which restricts access to RNA Polymerase II by an unknown mechanism. Taking a nuclear organization point of view, we showed that the male X chromosome resides in the pore proximal subnuclear compartment whereas the DCC bound to the X, inhibits this spatial organization in the hermaphrodites. Here we discuss our results and propose a model that reassigns the role of DCC from repression of genes to inhibition of activation.
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Affiliation(s)
- Rahul Sharma
- a Cell Fate and Nuclear Organization ; Institute of Cell Biology ; University of Bern ; Bern , Switzerland
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27
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Abstract
Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this vital role, NPC components influence genome functions in a transport-independent manner. Nups play an evolutionarily conserved role in gene expression regulation that, in metazoans, extends into the nuclear interior. Additionally, in proliferative cells, Nups play a crucial role in genome integrity maintenance and mitotic progression. Here we discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation.
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28
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Gay S, Foiani M. Nuclear envelope and chromatin, lock and key of genome integrity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 317:267-330. [PMID: 26008788 DOI: 10.1016/bs.ircmb.2015.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
More than as an inert separation between the inside and outside of the nucleus, the nuclear envelope (NE) constitutes an active toll, which controls the import and export of molecules, and also a hub for a diversity of genomic processes, such as transcription, DNA repair, and chromatin dynamics. Proteins localized at the inner surface of the NE (such as lamins, nuclear pore proteins, lamin-associated proteins) interact with chromatin in a dynamic manner, contributing to the establishment of topological domains. In this review, we address the complex interplay between chromatin and NE. We discuss the divergence of this cross talk during evolution and comment both on the current established models and the most recent findings. In particular, we focus our attention on how the NE cooperates with chromatin in protecting the genome integrity.
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Affiliation(s)
- Sophie Gay
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Marco Foiani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy; Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
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29
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Talamas JA, Capelson M. Nuclear envelope and genome interactions in cell fate. Front Genet 2015; 6:95. [PMID: 25852741 PMCID: PMC4365743 DOI: 10.3389/fgene.2015.00095] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 02/22/2015] [Indexed: 12/14/2022] Open
Abstract
The eukaryotic cell nucleus houses an organism’s genome and is the location within the cell where all signaling induced and development-driven gene expression programs are ultimately specified. The genome is enclosed and separated from the cytoplasm by the nuclear envelope (NE), a double-lipid membrane bilayer, which contains a large variety of trans-membrane and associated protein complexes. In recent years, research regarding multiple aspects of the cell nucleus points to a highly dynamic and coordinated concert of efforts between chromatin and the NE in regulation of gene expression. Details of how this concert is orchestrated and how it directs cell differentiation and disease are coming to light at a rapid pace. Here we review existing and emerging concepts of how interactions between the genome and the NE may contribute to tissue specific gene expression programs to determine cell fate.
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Affiliation(s)
- Jessica A Talamas
- Program in Epigenetics, Department of Cell and Developmental Biology, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Maya Capelson
- Program in Epigenetics, Department of Cell and Developmental Biology, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
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30
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Kasper DM, Wang G, Gardner KE, Johnstone TG, Reinke V. The C. elegans SNAPc component SNPC-4 coats piRNA domains and is globally required for piRNA abundance. Dev Cell 2015; 31:145-58. [PMID: 25373775 DOI: 10.1016/j.devcel.2014.09.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 08/25/2014] [Accepted: 09/25/2014] [Indexed: 11/26/2022]
Abstract
The Piwi/Piwi-interacting RNA (piRNA) pathway protects the germline from the activity of foreign sequences such as transposons. Remarkably, tens of thousands of piRNAs arise from a minimal number of discrete genomic regions. The extent to which clustering of these small RNA genes contributes to their coordinated expression remains unclear. We show that C. elegans SNPC-4, the Myb-like DNA-binding subunit of the small nuclear RNA activating protein complex, binds piRNA clusters in a germline-specific manner and is required for global piRNA expression. SNPC-4 localization is mutually dependent with localization of piRNA biogenesis factor PRDE-1. SNPC-4 exhibits an atypical widely distributed binding pattern that "coats" piRNA domains. Discrete peaks within the domains occur frequently at RNA-polymerase-III-occupied transfer RNA (tRNA) genes, which have been implicated in chromatin organization. We suggest that SNPC-4 binding establishes a positive expression environment across piRNA domains, providing an explanation for the conserved clustering of individually transcribed piRNA genes.
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Affiliation(s)
- Dionna M Kasper
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Guilin Wang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kathryn E Gardner
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Timothy G Johnstone
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Valerie Reinke
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
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31
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Vollmer B, Antonin W. The diverse roles of the Nup93/Nic96 complex proteins - structural scaffolds of the nuclear pore complex with additional cellular functions. Biol Chem 2014; 395:515-28. [PMID: 24572986 DOI: 10.1515/hsz-2013-0285] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/22/2014] [Indexed: 11/15/2022]
Abstract
Nuclear pore complexes mediate the transport between the cell nucleoplasm and cytoplasm. These 125 MDa structures are among the largest assemblies found in eukaryotes, built from proteins organized in distinct subcomplexes that act as building blocks during nuclear pore complex biogenesis. In this review, we focus on one of these subcomplexes, the Nup93 complex in metazoa and its yeast counterpart, the Nic96 complex. We discuss its essential function in nuclear pore complex assembly as a linker between the nuclear membrane and the central part of the pore and its various roles in nuclear transport processes and beyond.
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Sharma R, Jost D, Kind J, Gómez-Saldivar G, van Steensel B, Askjaer P, Vaillant C, Meister P. Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans. Genes Dev 2014; 28:2591-6. [PMID: 25452271 PMCID: PMC4248290 DOI: 10.1101/gad.248864.114] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/20/2014] [Indexed: 01/04/2023]
Abstract
The adjustment of X-linked gene expression to the X chromosome copy number (dosage compensation [DC]) has been widely studied as a model of chromosome-wide gene regulation. In Caenorhabditis elegans, DC is achieved by twofold down-regulation of gene expression from both Xs in hermaphrodites. We show that in males, the single X chromosome interacts with nuclear pore proteins, while in hermaphrodites, the DC complex (DCC) impairs this interaction and alters X localization. Our results put forward a structural model of DC in which X-specific sequences locate the X chromosome in transcriptionally active domains in males, while the DCC prevents this in hermaphrodites.
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Affiliation(s)
- Rahul Sharma
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Daniel Jost
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, UMR 5672, Centre National de la Recherche Scientifique (CNRS), 69007 Lyon, France
| | - Jop Kind
- Division of Gene Regulation, The Netherlands Cancer Institute, 1006 Amsterdam, The Netherlands
| | | | - Bas van Steensel
- Division of Gene Regulation, The Netherlands Cancer Institute, 1006 Amsterdam, The Netherlands
| | - Peter Askjaer
- Spanish National Research Council (CSIC), The Junta of Andalusia (JA), Universidad Pablo de Olavide, Andalusian Center for Developmental Biology (CABD), 41013 Sevilla, Spain
| | - Cédric Vaillant
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, UMR 5672, Centre National de la Recherche Scientifique (CNRS), 69007 Lyon, France
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland;
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Rijal K, Maraia RJ, Arimbasseri AG. A methods review on use of nonsense suppression to study 3' end formation and other aspects of tRNA biogenesis. Gene 2014; 556:35-50. [PMID: 25447915 DOI: 10.1016/j.gene.2014.11.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 12/26/2022]
Abstract
Suppressor tRNAs bear anticodon mutations that allow them to decode premature stop codons in metabolic marker gene mRNAs, that can be used as in vivo reporters of functional tRNA biogenesis. Here, we review key components of a suppressor tRNA system specific to Schizosaccharomyces pombe and its adaptations for use to study specific steps in tRNA biogenesis. Eukaryotic tRNA biogenesis begins with transcription initiation by RNA polymerase (pol) III. The nascent pre-tRNAs must undergo folding, 5' and 3' processing to remove the leader and trailer, nuclear export, and splicing if applicable, while multiple complex chemical modifications occur throughout the process. We review evidence that precursor-tRNA processing begins with transcription termination at the oligo(T) terminator element, which forms a 3' oligo(U) tract on the nascent RNA, a sequence-specific binding site for the RNA chaperone, La protein. The processing pathway bifurcates depending on a poorly understood property of pol III termination that determines the 3' oligo(U) length and therefore the affinity for La. We thus review the pol III termination process and the factors involved including advances using gene-specific random mutagenesis by dNTP analogs that identify key residues important for transcription termination in certain pol III subunits. The review ends with a 'technical approaches' section that includes a parts lists of suppressor-tRNA alleles, strains and plasmids, and graphic examples of its diverse uses.
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Affiliation(s)
- Keshab Rijal
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J Maraia
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Aneeshkumar G Arimbasseri
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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Abstract
Integral nuclear pore proteins associate with subsets of snoRNA and tRNA genes transcribed by RNA polymerase III and promote 3′ transcript processing in nematodes.
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35
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Chen M, Gartenberg MR. Coordination of tRNA transcription with export at nuclear pore complexes in budding yeast. Genes Dev 2014; 28:959-70. [PMID: 24788517 PMCID: PMC4018494 DOI: 10.1101/gad.236729.113] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along budding yeast chromosomes. Here, Chen and Gartenberg examined the spatial and temporal aspects of tRNA gene expression. Unexpectedly, they found that tRNA genes are transcribed in a periodic manner during cell cycle progression. Moreover, tRNA genes migrate to nuclear pore complexes when transcription peaks in M phase. This study demonstrates how RNA polymerase III-transcribed genes are gated to nuclear pore complexes in yeast. tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along the chromosomes of budding yeast. Existing evidence suggests that the genes congregate together at the nucleolus and/or centromeres. In this study, we re-examined spatial and temporal aspects of tRNA gene (tDNA) expression. We show that tDNA transcription fluctuates during cell cycle progression. In M phase, when tRNA synthesis peaks, tDNAs localize at nuclear pore complexes (NPCs). Docking of a tDNA requires the DNA sequence of the contacted gene, nucleoporins Nup60 and Nup2, and cohesin. Characterization of mutants that block NPC localization revealed that docking is a consequence of elevated tDNA transcription. NPC–tDNA contact falters in the absence of the principal exportin of nascent tRNA, Los1, and genetic assays indicate that gating of tDNAs at NPCs favors cytoplasmic accumulation of functional tRNA. Collectively, the data suggest that tDNAs associate with NPCs to coordinate RNA polymerase III transcription with the nuclear export of pre-tRNA. The M-phase specificity of NPC contact reflects a regulatory mechanism that may have evolved, in part, to avoid collisions between DNA replication forks and transcribing RNA polymerase III machinery at NPCs.
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Affiliation(s)
- Miao Chen
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, USA
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36
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Gruber AR. RNA Polymerase III promoter screen uncovers a novel noncoding RNA family conserved in Caenorhabditis and other clade V nematodes. Gene 2014; 544:236-40. [PMID: 24792899 DOI: 10.1016/j.gene.2014.04.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 10/25/2022]
Abstract
RNA Polymerase III is a highly specialized enzyme complex responsible for the transcription of a very distinct set of housekeeping noncoding RNAs including tRNAs, 7SK snRNA, Y RNAs, U6 snRNA, and the RNA components of RNaseP and RNaseMRP. In this work we have utilized the conserved promoter structure of known RNA Polymerase III transcripts consisting of characteristic sequence elements termed proximal sequence elements (PSE) A and B and a TATA-box to uncover a novel RNA Polymerase III-transcribed, noncoding RNA family found to be conserved in Caenorhabditis as well as other clade V nematode species. Homology search in combination with detailed sequence and secondary structure analysis revealed that members of this novel ncRNA family evolve rapidly, and only maintain a potentially functional small stem structure that links the 5' end to the very 3' end of the transcript and a small hairpin structure at the 3' end. This is most likely required for efficient transcription termination. In addition, our study revealed evidence that canonical C/D box snoRNAs are also transcribed from a PSE A-PSE B-TATA-box promoter in Caenorhabditis elegans.
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Affiliation(s)
- Andreas R Gruber
- Computational and Systems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
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37
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Ptak C, Aitchison JD, Wozniak RW. The multifunctional nuclear pore complex: a platform for controlling gene expression. Curr Opin Cell Biol 2014; 28:46-53. [PMID: 24657998 DOI: 10.1016/j.ceb.2014.02.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 02/21/2014] [Accepted: 02/22/2014] [Indexed: 12/21/2022]
Abstract
In addition to their established roles in nucleocytoplasmic transport, the intimate association of nuclear pore complexes (NPCs) with chromatin has long led to speculation that these structures influence peripheral chromatin structure and regulate gene expression. These ideas have their roots in morphological observations, however recent years have seen the identification of physical interactions between NPCs, chromatin, and the transcriptional machinery. Key insights into the molecular functions of specific NPC proteins have uncovered roles for these proteins in transcriptional activation and elongation, mRNA processing, as well as chromatin structure and localization. Here, we review recent studies that provide further molecular detail on the role of specific NPC components as distinct platforms for these chromatin dependent processes.
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Affiliation(s)
- Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John D Aitchison
- Seattle Biomedical Research Institute and Institute for Systems Biology, 307 Westlake Ave N, Seattle, WA 98109, USA.
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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38
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Pascual-Garcia P, Capelson M. Nuclear pores as versatile platforms for gene regulation. Curr Opin Genet Dev 2014; 25:110-7. [PMID: 24632227 DOI: 10.1016/j.gde.2013.12.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 12/18/2013] [Indexed: 12/30/2022]
Abstract
Functional compartmentalization of the genome relies on interactions between genomic regions and various nuclear scaffolds and macro-complexes. The Nuclear Pore Complex (NPC) is a large nuclear envelope-embedded protein complex, which creates a highly regulated transport channel between the nucleus and the cytoplasm. In addition to its central role in transport, the NPC has been linked to genome compartmentalization via binding to specific regions of the genome and association with gene regulatory machinery. Although originally proposed to preferentially associate with active genes, the NPC has now been implicated in both gene activating and gene silencing processes. Here, we review recent findings that highlight the roles of various components of the NPC in transcriptional activation, transcriptional memory, heterochromatin formation, post-transcriptional gene silencing and RNA processing. Together, these findings suggest that the nuclear pore is utilized as a regulatory platform for a number of distinct gene expression processes and further point to its central role in setting up particular expression environments on the genomic template.
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Affiliation(s)
- Pau Pascual-Garcia
- Department of Cell and Developmental Biology, University of Pennsylvania, 9-101 Smilow Center for Translational Research, 3400 Civic Center Blvd, Philadelphia, PA 19104, United States
| | - Maya Capelson
- Department of Cell and Developmental Biology, University of Pennsylvania, 9-101 Smilow Center for Translational Research, 3400 Civic Center Blvd, Philadelphia, PA 19104, United States.
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39
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Askjaer P, Galy V, Meister P. Modern Tools to Study Nuclear Pore Complexes and Nucleocytoplasmic Transport in Caenorhabditis elegans. Methods Cell Biol 2014; 122:277-310. [DOI: 10.1016/b978-0-12-417160-2.00013-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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40
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Nuclear organization: Processing at the pore. Nat Rev Mol Cell Biol 2013; 14:688. [PMID: 24088743 DOI: 10.1038/nrm3682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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