scholarly journals Isw2 and Ino80 chromatin remodeling factors regulate chromatin, replication, and copy number at the yeast ribosomal DNA locus

2018 ◽  
Author(s):  
Sam Cutler ◽  
Laura J Lee ◽  
Toshio Tsukiyama
Keyword(s):  
Chromatin Remodeling ◽  
Ribosomal Rna ◽  
Ribosomal Dna ◽  
Chromatin Structure ◽  
Copy Number ◽  
Rdna Repeat ◽  
Repeat Copy Number ◽  
Dependent Processes ◽  
Rna Genes ◽  
Repeat Copy

AbstractIn the budding yeast Saccharomyces cerevisiae, ribosomal RNA genes are encoded in a highly repetitive tandem array referred to as the ribosomal DNA (rDNA) locus. The yeast rDNA is the site of a diverse set of DNA-dependent processes, including transcription of ribosomal RNAs by RNA Polymerases I and III, transcription of non-coding RNAs by RNA Polymerase II, DNA replication initiation, replication fork blocking, and recombination-mediated regulation of rDNA repeat copy number. All of this takes place in the context of chromatin, but relatively little is known about the roles played by ATP-dependent chromatin remodeling factors at the yeast rDNA. In this work, we report that the Isw2 and Ino80 chromatin remodeling factors are targeted to this highly repetitive locus. We characterize for the first time their function in modifying local chromatin structure, finding that loss of these factors affects the occupancy of nucleosomes in the 35S ribosomal RNA gene and the positioning of nucleosomes flanking the ribosomal origin of replication. In addition, we report that Isw2 and Ino80 promote efficient firing of the ribosomal origin of replication and facilitate the regulated increase of rDNA repeat copy number. This work significantly expands our understanding of the importance of ATP-dependent chromatin remodeling for rDNA biology.Author SummaryTo satisfy high cellular demand for ribosomes, genomes contain many copies of the genes encoding the RNA components of ribosomes. In the budding yeast Saccharomyces cerevisiae, these ribosomal RNA genes are located in the “ribosomal DNA locus”, a highly repetitive array that contains approximately 150 copies of the same unit, in contrast to the single copies that suffice for most genes. This repetitive quality creates unique regulatory needs. Chromatin structure, the packaging and organization of DNA, is a critical determinant of DNA-dependent processes throughout the genome. ATP-dependent chromatin remodeling factors are important regulators of chromatin structure, and yet relatively little is known about how members of this class of protein affect DNA organization or behavior at the rDNA. In this work, we show that the Isw2 and Ino80 chromatin remodeling factors regulate two features of chromatin structure at the rDNA, the occupancy and the positioning of nucleosomes. In addition, we find that these factors regulate two critical processes that function uniquely at this locus: DNA replication originating from within the rDNA array, and the regulated increase of rDNA repeat copy number.

scholarly journals The Replication Fork Barrier Site Forms a Unique Structure with Fob1p and Inhibits the Replication Fork

2003 ◽  
Vol 23 (24) ◽  
pp. 9178-9188 ◽  
Author(s):  
Takehiko Kobayashi
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Copy Number ◽  
Replication Fork ◽  
Rrna Genes ◽  
Zinc Finger Motif ◽  
Rdna Repeat ◽  
Force Microscopy ◽  
Repeat Copy Number ◽  
Atomic Force ◽  
Repeat Copy

ABSTRACT The replication fork barrier site (RFB) is an ∼100-bp DNA sequence located near the 3′ end of the rRNA genes in the yeast Saccharomyces cerevisiae. The gene FOB1 is required for this RFB activity. FOB1 is also necessary for recombination in the ribosomal DNA (rDNA), including increase and decrease of rDNA repeat copy number, production of extrachromosomal rDNA circles, and possibly homogenization of the repeats. Despite the central role that Foblp plays in both replication fork blocking and rDNA recombination, the molecular mechanism by which Fob1p mediates these activities has not been determined. Here, I show by using chromatin immunoprecipitation, gel shift, footprinting, and atomic force microscopy assays that Fob1p directly binds to the RFB. Fob1p binds to two separated sequences in the RFB. A predicted zinc finger motif in Fob1p was shown to be essential for the RFB binding, replication fork blocking, and rDNA recombination activities. The RFB seems to wrap around Fob1p, and this wrapping structure may be important for function in the rDNA repeats.

scholarly journals Cell volume homeostatically controls the rDNA repeat copy number and rRNA synthesis rate in yeast

PLoS Genetics ◽  
2021 ◽  
Vol 17 (4) ◽  
pp. e1009520
Author(s):  
José E. Pérez-Ortín ◽  
Adriana Mena ◽  
Marina Barba-Aliaga ◽  
Abhyudai Singh ◽  
Sebastián Chávez ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Cell Volume ◽  
Copy Number ◽  
Rna Polymerase I ◽  
Synthesis Rate ◽  
Transcription Rate ◽  
Rdna Repeat ◽  
Repeat Copy Number ◽  
Polymerase I ◽  
Repeat Copy

The adjustment of transcription and translation rates to the changing needs of cells is of utmost importance for their fitness and survival. We have previously shown that the global transcription rate for RNA polymerase II in budding yeast Saccharomyces cerevisiae is regulated in relation to cell volume. Total mRNA concentration is constant with cell volume since global RNApol II-dependent nascent transcription rate (nTR) also keeps constant but mRNA stability increases with cell size. In this paper, we focus on the case of rRNA and RNA polymerase I. Contrarily to that found for RNA pol II, we detected that RNA polymerase I nTR increases proportionally to genome copies and cell size in polyploid cells. In haploid mutant cells with larger cell sizes, the rDNA repeat copy number rises. By combining mathematical modeling and experimental work with the large-size cln3 strain, we observed that the increasing repeat copy number is based on a feedback mechanism in which Sir2 histone deacetylase homeostatically controls the amplification of rDNA repeats in a volume-dependent manner. This amplification is paralleled with an increase in rRNA nTR, which indicates a control of the RNA pol I synthesis rate by cell volume.

scholarly journals Cell volume homeostatically controls the rDNA repeat copy number and rRNA synthesis rate in yeast

2019 ◽  
Author(s):  
José E. Pérez-Ortín ◽  
Adriana Mena ◽  
Marina Barba-Aliaga ◽  
Rebeca Alonso-Monge ◽  
Abhyudai Singh ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Cell Volume ◽  
Copy Number ◽  
Rna Polymerase I ◽  
Rrna Genes ◽  
Synthesis Rate ◽  
Rdna Repeat ◽  
Repeat Copy Number ◽  
Polymerase I ◽  
Repeat Copy

AbstractThe adjustment of transcription and translation rates to variable needs is of utmost importance for the fitness and survival of living cells. We have previously shown that the global transcription rate for RNA polymerase II is regulated differently in cells presenting symmetrical or asymmetrical cell division. The budding yeast Saccharomyces cerevisiae adopts a particular strategy to avoid that the smaller daughter cells increase their total mRNA concentration with every generation. The global mRNA synthesis rate lowers with a growing cell volume, but global mRNA stability increases. In this paper, we address what the solution is to the same theoretical problem for the RNA polymerase I synthesis rate. We find that the RNA polymerase I synthesis rate strictly depends on the copy number of its 35S rRNA gene. For cells with larger cell sizes, such as a mutant cln3 strain, the rDNA repeat copy number is increased by a mechanism based on a feed-back mechanism in which Sir2 histone deacetylase homeostatically controls the amplification of the rRNA genes at the rDNA locus in a volume-dependent manner.

scholarly journals Age-dependent ribosomal DNA variations and their effect on cellular function in mammalian cells

2020 ◽  
Author(s):  
Eriko Watada ◽  
Sihan Li ◽  
Yutaro Hori ◽  
Katsunori Fujiki ◽  
Katsuhiko Shirahige ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Copy Number ◽  
Mammalian Cells ◽  
Bone Marrow Cells ◽  
Budding Yeast ◽  
Rdna Repeat ◽  
Age Dependent ◽  
Old Mice ◽  
Rdna Copy ◽  
Rdna Copy Number

AbstractThe ribosomal RNA gene, which consists of tandem repetitive arrays (rDNA repeat), is one of the most unstable regions in the genome. The rDNA repeat in the budding yeast is known to become unstable as the cell ages. However, it is unclear how the rDNA repeat changes in ageing mammalian cells. Using quantitative analyses, we identified age-dependent alterations in rDNA copy number and levels of methylation in mice. The degree of methylation and copy number of rDNA from bone marrow cells of 2-year-old mice were increased by comparison to 4-week-old mice in two mouse strains, BALB/cA and C57BL/6. Moreover, the level of pre-rRNA transcripts was reduced in older BALB/cA mice. We also identified many sequence variations among the repeats with two mutations being unique to old mice. These sequences were conserved in budding yeast and equivalent mutations shortened the yeast chronological lifespan. Our findings suggest that rDNA is also fragile in mammalian cells and alterations within this region have a profound effect on cellular function.Author SummaryThe ribosomal RNA gene (rDNA) is one of the most unstable regions in the genome due to its tandem repetitive structure. rDNA copy number in the budding yeast increases and becomes unstable as the cell ages. It is speculated that the rDNA produces an “aging signal” inducing senescence and death. However, it is unclear how the rDNA repeat changes during the aging process in mammalian cells. In this study, we attempted to identify the age-dependent alteration of rDNA in mice. Using quantitative single cell analysis, we show that rDNA copy number increases in old mice bone marrow cells. By contrast, the level of ribosomal RNA production was reduced because of increased levels of DNA methylation that represses transcription. We also identified many sequence variations in the rDNA. Among them, three mutations were unique to old mice and two of them were found in the conserved region in budding yeast. We then established a yeast strain with the old mouse-specific mutations and found this shortened the lifespan of the cells. These findings suggest that rDNA is also fragile in mammalian cells and alteration to this region of the genome affects cellular senescence.

Variation in primary sequence and tandem repeat copy number among i-antigens of Ichthyophthirius multifiliis☆

2002 ◽  
Vol 120 (1) ◽  
pp. 93-106 ◽  
Author(s):  
Yuankai Lin ◽  
Tian Long Lin ◽  
Chia-Cheng Wang ◽  
Xuting Wang ◽  
Knut Stieger ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Copy Number ◽  
Ichthyophthirius Multifiliis ◽  
Primary Sequence ◽  
Repeat Copy Number ◽  
Repeat Copy

scholarly journals Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Deanna C Tremblay ◽  
Graham Alexander ◽  
Shawn Moseley ◽  
Brian P Chadwick
Keyword(s):  
Copy Number Variation ◽  
Human Genome ◽  
Tandem Repeat ◽  
Copy Number ◽  
Repeat Copy Number ◽  
Number Variation ◽  
Repeat Copy

Effect of location, organization, and repeat-copy number in satellite-DNA evolution

2009 ◽  
Vol 282 (4) ◽  
pp. 395-406 ◽  
Author(s):  
R. Navajas-Pérez ◽  
M. E. Quesada del Bosque ◽  
M. A. Garrido-Ramos
Keyword(s):  
Satellite Dna ◽  
Copy Number ◽  
Dna Evolution ◽  
Repeat Copy Number ◽  
Satellite Dna Evolution ◽  
Repeat Copy

The Tomato Cf-5 Disease Resistance Gene and Six Homologs Show Pronounced Allelic Variation in Leucine-Rich Repeat Copy Number

1998 ◽  
Vol 10 (11) ◽  
pp. 1915
Author(s):  
Mark S. Dixon ◽  
Kostas Hatzixanthis ◽  
David A. Jones ◽  
Kate Harrison ◽  
Jonathan D. G. Jones
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Copy Number ◽  
Allelic Variation ◽  
Disease Resistance Gene ◽  
Leucine Rich Repeat ◽  
Repeat Copy Number ◽  
Repeat Copy

scholarly journals Heritability and Variability in Ribosomal RNA Genes of Vicia faba

Genetics ◽  
1987 ◽  
Vol 117 (2) ◽  
pp. 285-295
Author(s):  
Scott O Rogers ◽  
Arnold J Bendich
Keyword(s):  
Vicia Faba ◽  
Ribosomal Rna ◽  
Copy Number ◽  
Nearest Neighbor ◽  
Blot Hybridization ◽  
Ribosomal Rna Genes ◽  
Hybridization Pattern ◽  
Nontranscribed Spacer ◽  
Rna Genes ◽  
Eco Ri

ABSTRACT We have compared the restriction patterns and copy numbers of ribosomal RNA genes (rDNA) between and within individuals of Vicia faba. While the Eco RI blot-hybridization patterns changed only after one to two generations, copy number changes were found among different tissues of the same plant. Copy number differences among individuals in the population were as great as 95-fold, whereas as much as a 12-fold variation was seen among tissues of the same plant. Among individual F1 progeny from genetic crosses, nearly an 8-fold variation was seen, and among individuals of the F2 generation a spread of 22-fold was measured. Among individual siblings of self-pollinated parents, up to 7-fold variation was observed. However, changes in copy number did not necessarily indicate changes in rDNA Eco RI blot-hybridization pattern, and vice versa. Furthermore, nearest neighbor analysis of R-loop experiments showed that the arrangement of members of the "nontranscribed" spacer (NTS) size classes along the chromosome was not random, but some clustering was indicated. The data are consistent with the hypothesis that sister chromatid exchange in somatic cells of V. faba is the primary mechanism for altering the rDNA copy number as well as causing the extreme variation observed in the NTS. Variation among individuals in rDNA blot-hybridization pattern was also observed for Vicia villosa, Vicia dasycarpa, Vicia benghalensis and Vicia pannonica.

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