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Kim JH, Nagaraja R, Ogurtsov AY, Noskov VN, Liskovykh M, Lee HS, Hori Y, Kobayashi T, Hunter K, Schlessinger D, Kouprina N, Shabalina SA, Larionov V. Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability. NAR Genom Bioinform 2024; 6:lqae070. [PMID: 38881577 PMCID: PMC11177557 DOI: 10.1093/nargab/lqae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/20/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
Ribosomal DNA (rDNA) repeat units are organized into tandem clusters in eukaryotic cells. In mice, these clusters are located on at least eight chromosomes and show extensive variation in the number of repeats between mouse genomes. To analyze intra- and inter-genomic variation of mouse rDNA repeats, we selectively isolated 25 individual rDNA units using Transformation-Associated Recombination (TAR) cloning. Long-read sequencing and subsequent comparative sequence analysis revealed that each full-length unit comprises an intergenic spacer (IGS) and a ∼13.4 kb long transcribed region encoding the three rRNAs, but with substantial variability in rDNA unit size, ranging from ∼35 to ∼46 kb. Within the transcribed regions of rDNA units, we found 209 variants, 70 of which are in external transcribed spacers (ETSs); but the rDNA size differences are driven primarily by IGS size heterogeneity, due to indels containing repetitive elements and some functional signals such as enhancers. Further evolutionary analysis categorized rDNA units into distinct clusters with characteristic IGS lengths; numbers of enhancers; and presence/absence of two common SNPs in promoter regions, one of which is located within promoter (p)RNA and may influence pRNA folding stability. These characteristic features of IGSs also correlated significantly with 5'ETS variant patterns described previously and associated with differential expression of rDNA units. Our results suggest that variant rDNA units are differentially regulated and open a route to investigate the role of rDNA variation on nucleolar formation and possible associations with pathology.
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Affiliation(s)
- Jung-Hyun Kim
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Ramaiah Nagaraja
- National Institute of Aging, Laboratory of Genetics and Genomics, Baltimore, MD, USA
| | - Alexey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Vladimir N Noskov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Mikhail Liskovykh
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Hee-Sheung Lee
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Yutaro Hori
- The University of Tokyo, Laboratory of Genome Regeneration, Tokyo 113-0032, Japan
| | - Takehiko Kobayashi
- The University of Tokyo, Laboratory of Genome Regeneration, Tokyo 113-0032, Japan
| | - Kent Hunter
- National Cancer Institute, Laboratory of Cancer Biology and Genetics, Bethesda, MD, USA
| | - David Schlessinger
- National Institute of Aging, Laboratory of Genetics and Genomics, Baltimore, MD, USA
| | - Natalay Kouprina
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Vladimir Larionov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
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2
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Shatskikh AS, Fefelova EA, Klenov MS. Functions of RNAi Pathways in Ribosomal RNA Regulation. Noncoding RNA 2024; 10:19. [PMID: 38668377 PMCID: PMC11054153 DOI: 10.3390/ncrna10020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.
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Affiliation(s)
- Aleksei S. Shatskikh
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia;
| | - Elena A. Fefelova
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Mikhail S. Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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Annapragada AV, Niknafs N, White JR, Bruhm DC, Cherry C, Medina JE, Adleff V, Hruban C, Mathios D, Foda ZH, Phallen J, Scharpf RB, Velculescu VE. Genome-wide repeat landscapes in cancer and cell-free DNA. Sci Transl Med 2024; 16:eadj9283. [PMID: 38478628 DOI: 10.1126/scitranslmed.adj9283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
Genetic changes in repetitive sequences are a hallmark of cancer and other diseases, but characterizing these has been challenging using standard sequencing approaches. We developed a de novo kmer finding approach, called ARTEMIS (Analysis of RepeaT EleMents in dISease), to identify repeat elements from whole-genome sequencing. Using this method, we analyzed 1.2 billion kmers in 2837 tissue and plasma samples from 1975 patients, including those with lung, breast, colorectal, ovarian, liver, gastric, head and neck, bladder, cervical, thyroid, or prostate cancer. We identified tumor-specific changes in these patients in 1280 repeat element types from the LINE, SINE, LTR, transposable element, and human satellite families. These included changes to known repeats and 820 elements that were not previously known to be altered in human cancer. Repeat elements were enriched in regions of driver genes, and their representation was altered by structural changes and epigenetic states. Machine learning analyses of genome-wide repeat landscapes and fragmentation profiles in cfDNA detected patients with early-stage lung or liver cancer in cross-validated and externally validated cohorts. In addition, these repeat landscapes could be used to noninvasively identify the tissue of origin of tumors. These analyses reveal widespread changes in repeat landscapes of human cancers and provide an approach for their detection and characterization that could benefit early detection and disease monitoring of patients with cancer.
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Affiliation(s)
- Akshaya V Annapragada
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Noushin Niknafs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - James R White
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Daniel C Bruhm
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Christopher Cherry
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jamie E Medina
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Vilmos Adleff
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Carolyn Hruban
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Dimitrios Mathios
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Zachariah H Foda
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jillian Phallen
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Robert B Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Victor E Velculescu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Dyomin A, Galkina S, Ilina A, Gaginskaya E. Single Copies of the 5S rRNA Inserted into 45S rDNA Intergenic Spacers in the Genomes of Nototheniidae (Perciformes, Actinopterygii). Int J Mol Sci 2023; 24:ijms24087376. [PMID: 37108537 PMCID: PMC10138776 DOI: 10.3390/ijms24087376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
In the vast majority of Animalia genomes, the 5S rRNA gene repeats are located on chromosomes outside of the 45S rDNA arrays of the nucleolar organiser (NOR). We analysed the genomic databases available and found that a 5S rDNA sequence is inserted into the intergenic spacer (IGS) between the 45S rDNA repeats in ten species of the family Nototheniidae (Perciformes, Actinopterigii). We call this sequence the NOR-5S rRNA gene. Along with Testudines and Crocodilia, this is the second case of a close association between four rRNA genes within one repetitive unit in deuterostomes. In both cases, NOR-5S is oriented opposite the 45S rDNA. None of the three nucleotide substitutions compared to the canonical 5S rRNA gene influenced the 5S rRNA secondary structure. In transcriptomes of the Patagonian toothfish, we only found NOR-5S rRNA reads in ovaries and early embryos, but not in testis or somatic tissues of adults. Thus, we consider the NOR-5S gene to be a maternal-type 5S rRNA template. The colocalization of the 5S and 45S ribosomal genes appears to be essential for the equimolar production of all four rRNAs in the species that show rDNA amplification during oogenesis. Most likely, the integration of 5S and NOR rRNA genes occurred prior to Nototheniidae lineage diversification.
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Affiliation(s)
- Alexander Dyomin
- Biological Faculty, St. Petersburg State University, Universitetskaya Emb. 7/9, St. Petersburg 199034, Russia
| | - Svetlana Galkina
- Biological Faculty, St. Petersburg State University, Universitetskaya Emb. 7/9, St. Petersburg 199034, Russia
| | - Arina Ilina
- Biological Faculty, St. Petersburg State University, Universitetskaya Emb. 7/9, St. Petersburg 199034, Russia
| | - Elena Gaginskaya
- Biological Faculty, St. Petersburg State University, Universitetskaya Emb. 7/9, St. Petersburg 199034, Russia
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Variability of Human rDNA and Transcription Activity of the Ribosomal Genes. Int J Mol Sci 2022; 23:ijms232315195. [PMID: 36499515 PMCID: PMC9740796 DOI: 10.3390/ijms232315195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Human ribosomal DNA is represented by hundreds of repeats in each cell. Every repeat consists of two parts: a 13 kb long 47S DNA with genes encoding 18S, 5.8S, and 28S RNAs of ribosomal particles, and a 30 kb long intergenic spacer (IGS). Remarkably, transcription does not take place in all the repeats. The transcriptionally silent genes are characterized by the epigenetic marks of the inactive chromatin, including DNA hypermethylation of the promoter and adjacent areas. However, it is still unknown what causes the differentiation of the genes into active and silent. In this study, we examine whether this differentiation is related to the nucleotide sequence of IGS. We isolated ribosomal DNA from the nucleoli of human-derived HT1080 cells, and separated methylated and non-methylated DNA by chromatin immunoprecipitation. Then, we used PCR to amplify a 2 kb long region upstream of the transcription start and sequenced the product. We found that six SNVs and a series of short deletions in a region of simple repeats correlated with the DNA methylation status. These data indicate that variability of IGS sequence may initiate silencing of the ribosomal genes. Our study also suggests a number of pathways to this silencing that involve micro-RNAs and/or non-canonical DNA structures.
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Fefelova EA, Pleshakova IM, Mikhaleva EA, Pirogov SA, Poltorachenko V, Abramov Y, Romashin D, Shatskikh A, Blokh R, Gvozdev V, Klenov M. Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon. Nucleic Acids Res 2022; 50:867-884. [PMID: 35037046 PMCID: PMC8789037 DOI: 10.1093/nar/gkab1276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/21/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic genomes harbor hundreds of rRNA genes, many of which are transcriptionally silent. However, little is known about selective regulation of individual rDNA units. In Drosophila melanogaster, some rDNA repeats contain insertions of the R2 retrotransposon, which is capable to be transcribed only as part of pre-rRNA molecules. rDNA units with R2 insertions are usually inactivated, although R2 expression may be beneficial in cells with decreased rDNA copy number. Here we found that R2-inserted rDNA units are enriched with HP1a and H3K9me3 repressive mark, whereas disruption of the heterochromatin components slightly affects their silencing in ovarian germ cells. Surprisingly, we observed a dramatic upregulation of R2-inserted rRNA genes in ovaries lacking Udd (Under-developed) or other subunits (TAF1b and TAF1c-like) of the SL1-like complex, which is homologues to mammalian Selective factor 1 (SL1) involved in rDNA transcription initiation. Derepression of rRNA genes with R2 insertions was accompanied by a reduction of H3K9me3 and HP1a enrichment. We suggest that the impairment of the SL1-like complex affects a mechanism of selective activation of intact rDNA units which competes with heterochromatin formation. We also propose that R2 derepression may serve as an adaptive response to compromised rRNA synthesis.
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Affiliation(s)
- Elena A Fefelova
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena 91125, USA
| | - Irina M Pleshakova
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
- Laboratory for Neurobiology of Memory, P.K. Anokhin Institute of Normal Physiology, Moscow 125315, Russia
| | - Elena A Mikhaleva
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Sergei A Pirogov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Valentin A Poltorachenko
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Yuri A Abramov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Daniil D Romashin
- Laboratory of Precision Biosystems, V. N. Orekhovich Institute of Biomedical Chemistry, 10 Pogodinskaya St., Moscow 119121, Russia
| | - Aleksei S Shatskikh
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Roman S Blokh
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
- Department of Functional Genomics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova Street, Moscow 119334, Russia
| | - Vladimir A Gvozdev
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Mikhail S Klenov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
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Cockrell AJ, Gerton JL. Nucleolar Organizer Regions as Transcription-Based Scaffolds of Nucleolar Structure and Function. Results Probl Cell Differ 2022; 70:551-580. [PMID: 36348121 DOI: 10.1007/978-3-031-06573-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Eukaryotic genomes maintain multiple copies of ribosomal DNA gene repeats in tandem arrays to provide sufficient ribosomal RNAs to make ribosomes. These DNA repeats are the most highly transcribed regions of the genome, with dedicated transcriptional machinery to manage the enormous task of producing more than 50% of the total RNA in a proliferating cell. The arrays are called nucleolar organizer regions (NORs) and constitute the scaffold of the nucleolar compartment, where ribosome biogenesis occurs. Advances in molecular and cellular biology have brought great insights into how these arrays are transcribed and organized within genomes. Much of their biology is driven by their high transcription level, which has also driven the development of unique methods to understand rDNA gene activity, beginning with classic techniques such as silver staining and Miller spreads. However, the application of modern methodologies such as CRISPR gene editing, super-resolution microscopy, and long-read sequencing has enabled recent advances described herein, with many more discoveries possible soon. This chapter highlights what is known about NOR transcription and organization and the techniques applied historically and currently. Given the potential for NORs to impact organismal health and disease, as highlighted at the end of the chapter, the field must continue to develop and apply innovative analysis to understand genetic, epigenetic, and organizer properties of the ribosomal DNA repeats.
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Affiliation(s)
- Alexandria J Cockrell
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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Abstract
In human cells, each rDNA unit consists of the ~13 kb long ribosomal part and ~30 kb long intergenic spacer (IGS). The ribosomal part, transcribed by RNA polymerase I (pol I), includes genes coding for 18S, 5.8S, and 28S RNAs of the ribosomal particles, as well as their four transcribed spacers. Being highly repetitive, intensively transcribed, and abundantly methylated, rDNA is a very fragile site of the genome, with high risk of instability leading to cancer. Multiple small mutations, considerable expansion or contraction of the rDNA locus, and abnormally enhanced pol I transcription are usual symptoms of transformation. Recently it was found that both IGS and the ribosomal part of the locus contain many functional/potentially functional regions producing non-coding RNAs, which participate in the pol I activity regulation, stress reactions, and development of the malignant phenotype. Thus, there are solid reasons to believe that rDNA locus plays crucial role in carcinogenesis. In this review we discuss the data concerning the human rDNA and its closely associated factors as both targets and drivers of the pathways essential for carcinogenesis. We also examine whether variability in the structure of the locus may be blamed for the malignant transformation. Additionally, we consider the prospects of therapy focused on the activity of rDNA.
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Franek M, Kilar A, Fojtík P, Olšinová M, Benda A, Rotrekl V, Dvořáčková M, Fajkus J. Super-resolution microscopy of chromatin fibers and quantitative DNA methylation analysis of DNA fiber preparations. J Cell Sci 2021; 134:jcs258374. [PMID: 34350964 DOI: 10.1242/jcs.258374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Analysis of histone variants and epigenetic marks is dominated by genome-wide approaches in the form of chromatin immunoprecipitation-sequencing (ChIP-seq) and related methods. Although uncontested in their value for single-copy genes, mapping the chromatin of DNA repeats is problematic for biochemical techniques that involve averaging of cell populations or analysis of clusters of tandem repeats in a single-cell analysis. Extending chromatin and DNA fibers allows us to study the epigenetics of individual repeats in their specific chromosomal context, and thus constitutes an important tool for gaining a complete understanding of the epigenetic organization of genomes. We report that using an optimized fiber extension protocol is essential in order to obtain more reproducible data and to minimize the clustering of fibers. We also demonstrate that the use of super-resolution microscopy is important for reliable evaluation of the distribution of histone modifications on individual fibers. Furthermore, we introduce a custom script for the analysis of methylation levels on DNA fibers and apply it to map the methylation of telomeres, ribosomal genes and centromeres.
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Affiliation(s)
- Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137 Brno, Czech Republic
| | - Petr Fojtík
- International Clinical Research Center (ICRC) at St. Anne's University Hospital, Pekařská 53, CZ-65691 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Marie Olšinová
- Charles University, Faculty of Science, Biology Section, Imaging methods core facility at BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Aleš Benda
- Charles University, Faculty of Science, Biology Section, Imaging methods core facility at BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Vladimír Rotrekl
- International Clinical Research Center (ICRC) at St. Anne's University Hospital, Pekařská 53, CZ-65691 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jíří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137 Brno, Czech Republic
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Kint S, Van Criekinge W, Vandekerckhove L, De Vos WH, Bomsztyk K, Krause DS, Denisenko O. Single cell epigenetic visualization assay. Nucleic Acids Res 2021; 49:e43. [PMID: 33511400 PMCID: PMC8096246 DOI: 10.1093/nar/gkab009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 12/28/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
Characterization of the epigenetic status of individual cells remains a challenge. Current sequencing approaches have limited coverage, and it is difficult to assign an epigenetic status to the transcription state of individual gene alleles in the same cell. To address these limitations, a targeted microscopy-based epigenetic visualization assay (EVA) was developed for detection and quantification of epigenetic marks at genes of interest in single cells. The assay is based on an in situ biochemical reaction between an antibody-conjugated alkaline phosphatase bound to the epigenetic mark of interest, and a 5'-phosphorylated fluorophore-labeled DNA oligo tethered to a target gene by gene-specific oligonucleotides. When the epigenetic mark is present at the gene, phosphate group removal by the phosphatase protects the oligo from λ-exonuclease activity providing a quantitative fluorescent readout. We applied EVA to measure 5-methylcytosine (5mC) and H3K9Ac levels at different genes and the HIV-1 provirus in human cell lines. To link epigenetic marks to gene transcription, EVA was combined with RNA-FISH. Higher 5mC levels at the silenced compared to transcribed XIST gene alleles in female somatic cells validated this approach and demonstrated that EVA can be used to relate epigenetic marks to the transcription status of individual gene alleles.
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Affiliation(s)
- Sam Kint
- Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Winnok H De Vos
- Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Karol Bomsztyk
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Diane S Krause
- Depts. of Laboratory Medicine, Pathology and Cell Biology; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Oleg Denisenko
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
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11
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Smirnov E, Chmúrčiaková N, Liška F, Bažantová P, Cmarko D. Variability of Human rDNA. Cells 2021; 10:cells10020196. [PMID: 33498263 PMCID: PMC7909238 DOI: 10.3390/cells10020196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
In human cells, ribosomal DNA (rDNA) is arranged in ten clusters of multiple tandem repeats. Each repeat is usually described as consisting of two parts: the 13 kb long ribosomal part, containing three genes coding for 18S, 5.8S and 28S RNAs of the ribosomal particles, and the 30 kb long intergenic spacer (IGS). However, this standard scheme is, amazingly, often altered as a result of the peculiar instability of the locus, so that the sequence of each repeat and the number of the repeats in each cluster are highly variable. In the present review, we discuss the causes and types of human rDNA instability, the methods of its detection, its distribution within the locus, the ways in which it is prevented or reversed, and its biological significance. The data of the literature suggest that the variability of the rDNA is not only a potential cause of pathology, but also an important, though still poorly understood, aspect of the normal cell physiology.
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12
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Frank L, Rippe K. Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation. J Mol Biol 2020; 432:4270-4286. [DOI: 10.1016/j.jmb.2020.04.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022]
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13
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Maiser A, Dillinger S, Längst G, Schermelleh L, Leonhardt H, Németh A. Super-resolution in situ analysis of active ribosomal DNA chromatin organization in the nucleolus. Sci Rep 2020; 10:7462. [PMID: 32366902 PMCID: PMC7198602 DOI: 10.1038/s41598-020-64589-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Ribosomal RNA (rRNA) transcription by RNA polymerase I (Pol I) is the first key step of ribosome biogenesis. While the molecular mechanisms of rRNA transcription regulation have been elucidated in great detail, the functional organization of the multicopy rRNA gene clusters (rDNA) in the nucleolus is less well understood. Here we apply super-resolution 3D structured illumination microscopy (3D-SIM) to investigate the spatial organization of transcriptionally competent active rDNA chromatin at size scales well below the diffraction limit by optical microscopy. We identify active rDNA chromatin units exhibiting uniformly ring-shaped conformations with diameters of ~240 nm in mouse and ~170 nm in human fibroblasts, consistent with rDNA looping. The active rDNA chromatin units are clearly separated from each other and from the surrounding areas of rRNA processing. Simultaneous imaging of all active genes bound by Pol I and the architectural chromatin protein Upstream Binding Transcription Factor (UBF) reveals a random spatial orientation of regular repeats of rDNA coding sequences within the nucleoli. These observations imply rDNA looping and exclude potential formation of systematic spatial assemblies of the well-ordered repetitive arrays of transcription units. Collectively, this study uncovers key features of the 3D organization of active rDNA chromatin units and their nucleolar clusters providing a spatial framework of nucleolar chromatin organization at unprecedented detail.
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Affiliation(s)
- Andreas Maiser
- Department of Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Stefan Dillinger
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Gernot Längst
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Lothar Schermelleh
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Attila Németh
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany.
- Institute of Neuropathology, Justus Liebig University, Giessen, Germany.
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14
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Life time of some RNA products of rDNA intergenic spacer in HeLa cells. Histochem Cell Biol 2019; 152:271-280. [DOI: 10.1007/s00418-019-01804-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2019] [Indexed: 12/21/2022]
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15
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Pirogov SA, Gvozdev VA, Klenov MS. Long Noncoding RNAs and Stress Response in the Nucleolus. Cells 2019; 8:cells8070668. [PMID: 31269716 PMCID: PMC6678565 DOI: 10.3390/cells8070668] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) perform diverse functions in the regulation of cellular processes. Here we consider a variety of lncRNAs found in the ribosome production center, the nucleolus, and focus on their role in the response to environmental stressors. Nucleolar lncRNAs ensure stress adaptation by cessation of resource-intensive ribosomal RNA (rRNA) synthesis and by inducing the massive sequestration of proteins within the nucleolus. Different cell states like quiescence and cancer are also controlled by specific lncRNAs in the nucleolus. Taken together, recent findings allow us to consider lncRNAs as multifunctional regulators of nucleolar activities, which are responsive to various physiological conditions.
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Affiliation(s)
- Sergei A Pirogov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Vladimir A Gvozdev
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia.
| | - Mikhail S Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia.
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16
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The chromatin landscape of the ribosomal RNA genes in mouse and human. Chromosome Res 2019; 27:31-40. [PMID: 30617621 DOI: 10.1007/s10577-018-09603-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/21/2018] [Accepted: 12/26/2018] [Indexed: 12/21/2022]
Abstract
The rRNA genes of mouse and human encode the three major RNAs of the ribosome and as such are essential for growth and development. These genes are present in high copy numbers and arranged as direct repeats at the Nucleolar Organizer Regions on multiple chromosomes. Not all the rRNA genes are transcriptionally active, but the molecular mechanisms that determine activity are complex and still poorly understood. Recent studies applying a novel Deconvolution Chromatin Immunoprecipitation (DChIP-Seq) technique in conjunction with conditional gene inactivation provide new insights into the structure of the active rRNA genes and question previous assumptions on the role of chromatin and histone modifications. We suggest an alternative model for the active rRNA gene chromatin and discuss how this structure is determined and maintained.
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17
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Li B, Kremling KAG, Wu P, Bukowski R, Romay MC, Xie E, Buckler ES, Chen M. Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation. Genome Res 2018; 28:1555-1565. [PMID: 30166407 PMCID: PMC6169892 DOI: 10.1101/gr.229716.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 08/29/2018] [Indexed: 12/16/2022]
Abstract
Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variation present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA (rDNA) copy number and ribosomal RNA (rRNA) expression for a population of maize inbred lines and investigated the potential role of rDNA and rRNA dosage in regulating global gene expression. Extensive variation was found in both ribosomal DNA copy number and ribosomal RNA expression among maize inbred lines. However, rRNA abundance was not consistent with the copy number of the rDNA. We have not found that the rDNA gene dosage has a regulatory role in gene expression; however, thousands of genes are identified to be coregulated with rRNA expression, including genes participating in ribosome biogenesis and other functionally relevant pathways. We further investigated the potential roles of copy number and the expression level of rDNA on agronomic traits and found that both correlated with flowering time but through different regulatory mechanisms. This comprehensive analysis suggested that rRNA expression variation is a valuable source of functional diversity that affects gene expression variation and field-based phenotypic changes.
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Affiliation(s)
- Bo Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Karl A G Kremling
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Penghao Wu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- College of Agronomy, Xinjiang Agriculture University, Urumqi, China 830052
| | - Robert Bukowski
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York 14853, USA
| | - Maria C Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - En Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
- US Department of Agriculture-Agricultural Research Service (USDA-ARS), Ithaca, New York 14853, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
- University of Chinese Academy of Sciences, Beijing, China 100049
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18
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Abstract
The nucleolus as site of ribosome biogenesis holds a pivotal role in cell metabolism. It is composed of ribosomal DNA (rDNA), which is present as tandem arrays located in nucleolus organizer regions (NORs). In interphase cells, rDNA can be found inside and adjacent to nucleoli and the location is indicative for transcriptional activity of ribosomal genes-inactive rDNA (outside) versus active one (inside). Moreover, the nucleolus itself acts as a spatial organizer of non-nucleolar chromatin. Microscopy-based approaches offer the possibility to explore the spatially distinct localization of the different DNA populations in relation to the nucleolar structure. Recent technical developments in microscopy and preparatory methods may further our understanding of the functional architecture of nucleoli. This review will attempt to summarize the current understanding of mammalian nucleolar chromatin organization as seen from a microscopist's perspective.
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Affiliation(s)
- Christian Schöfer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
| | - Klara Weipoltshammer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
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19
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Hornáček M, Kováčik L, Mazel T, Cmarko D, Bártová E, Raška I, Smirnov E. Fluctuations of pol I and fibrillarin contents of the nucleoli. Nucleus 2017. [PMID: 28622108 DOI: 10.1080/19491034.2017.1306160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Nucleoli are formed on the basis of ribosomal DNA (rDNA) clusters called Nucleolus Organizer Regions (NORs). Each NOR contains multiple genes coding for RNAs of the ribosomal particles. The prominent components of the nucleolar ultrastructure, fibrillar centers (FC) and dense fibrillar components (DFC), together compose FC/DFC units. These units are centers of rDNA transcription by RNA polymerase I (pol I), as well as the early processing events, in which an essential role belongs to fibrillarin. Each FC/DFC unit probably corresponds to a single transcriptionally active gene. In this work, we transfected human-derived cells with GFP-RPA43 (subunit of pol I) and RFP-fibrillarin. Following changes of the fluorescent signals in individual FC/DFC units, we found two kinds of kinetics: 1) the rapid fluctuations with periods of 2-3 min, when the pol I and fibrillarin signals oscillated in anti-phase manner, and the intensities of pol I in the neighboring FC/DFC units did not correlate. 2) fluctuations with periods of 10 to 60 min, in which pol I and fibrillarin signals measured in the same unit did not correlate, but pol I signals in the units belonging to different nucleoli were synchronized. Our data indicate that a complex pulsing activity of transcription as well as early processing is common for ribosomal genes.
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Affiliation(s)
- M Hornáček
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University, and General University Hospital in Prague , Prague , Czech Republic
| | - L Kováčik
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University, and General University Hospital in Prague , Prague , Czech Republic
| | - T Mazel
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University, and General University Hospital in Prague , Prague , Czech Republic
| | - D Cmarko
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University, and General University Hospital in Prague , Prague , Czech Republic
| | - E Bártová
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University, and General University Hospital in Prague , Prague , Czech Republic.,b Institute of Biophysics of the CAS , Brno , Czech Republic
| | - I Raška
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University, and General University Hospital in Prague , Prague , Czech Republic
| | - E Smirnov
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University, and General University Hospital in Prague , Prague , Czech Republic
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20
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Dillinger S, Straub T, Németh A. Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation. PLoS One 2017; 12:e0178821. [PMID: 28575119 PMCID: PMC5456395 DOI: 10.1371/journal.pone.0178821] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/21/2017] [Indexed: 01/10/2023] Open
Abstract
Mammalian chromosomes are organized in structural and functional domains of 0.1–10 Mb, which are characterized by high self-association frequencies in the nuclear space and different contact probabilities with nuclear sub-compartments. They exhibit distinct chromatin modification patterns, gene expression levels and replication timing. Recently, nucleolus-associated chromosomal domains (NADs) have been discovered, yet their precise genomic organization and dynamics are still largely unknown. Here, we use nucleolus genomics and single-cell experiments to address these questions in human embryonic fibroblasts during replicative senescence. Genome-wide mapping reveals 1,646 NADs in proliferating cells, which cover about 38% of the annotated human genome. They are mainly heterochromatic and correlate with late replicating loci. Using Hi-C data analysis, we show that interactions of NADs dominate interphase chromosome contacts in the 10–50 Mb distance range. Interestingly, only minute changes in nucleolar association are observed upon senescence. These spatial rearrangements in subdomains smaller than 100 kb are accompanied with local transcriptional changes. In contrast, large centromeric and pericentromeric satellite repeat clusters extensively dissociate from nucleoli in senescent cells. Accordingly, H3K9me3-marked heterochromatin gets remodelled at the perinucleolar space as revealed by immunofluorescence analyses. Collectively, this study identifies connections between the nucleolus, 3D genome structure, and cellular aging at the level of interphase chromosome organization.
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Affiliation(s)
- Stefan Dillinger
- Biochemistry Center Regensburg, University of Regensburg, Regensburg, Germany
| | - Tobias Straub
- Biomedical Center, Bioinformatics, Ludwig-Maximilians-University, Munich, Germany
| | - Attila Németh
- Biochemistry Center Regensburg, University of Regensburg, Regensburg, Germany
- * E-mail: ,
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21
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Abstract
Nucleoli are formed on the basis of ribosomal genes coding for RNAs of ribosomal particles, but also include a great variety of other DNA regions. In this article, we discuss the characteristics of ribosomal DNA: the structure of the rDNA locus, complex organization and functions of the intergenic spacer, multiplicity of gene copies in one cell, selective silencing of genes and whole gene clusters, relation to components of nucleolar ultrastructure, specific problems associated with replication. We also review current data on the role of non-ribosomal DNA in the organization and function of nucleoli. Finally, we discuss probable causes preventing efficient visualization of DNA in nucleoli.
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22
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Abstract
Gene expression control is a fundamental determinant of cellular life with transcription being the most important step. The spatial nuclear arrangement of the transcription process driven by RNA polymerases II and III is nonrandomly organized in foci, which is believed to add another regulatory layer on gene expression control. RNA polymerase I transcription takes place within a specialized organelle, the nucleolus. Transcription of ribosomal RNA directly responds to metabolic requirements, which in turn is reflected in the architecture of nucleoli. It differs from that of the other polymerases with respect to the gene template organization, transcription rate, and epigenetic expression control, whereas other features are shared like the formation of DNA loops bringing genes and components of the transcription machinery in close proximity. In recent years, significant advances have been made in the understanding of the structural prerequisites of nuclear transcription, of the arrangement in the nuclear volume, and of the dynamics of these entities. Here, we compare ribosomal RNA and mRNA transcription side by side and review the current understanding focusing on structural aspects of transcription foci, of their constituents, and of the dynamical behavior of these components with respect to foci formation, disassembly, and cell cycle.
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Affiliation(s)
- Klara Weipoltshammer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
| | - Christian Schöfer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
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