• Pol II, assisted by the neurodegeneration-associated enzyme senataxin, generates a shield comprising triplex nucleic acid structures known as R-loops at intergenic spacers flanking nucleolar rRNA genes. (nature.com)
  • Within rDNA, rRNA genes are separated by large intergenic spacers (IGSs) (Extended Data Fig. 1a ). (nature.com)
  • Both classes of ribosomal genes appeared to be spread out to multiple chromosomal locations, i.e. the 45S and 5S rDNA clusters were detected on six and seven chromosome pairs, respectively. (scielo.br)
  • Uniparental silencing of 35S rRNA genes (rDNA), known as nucleolar dominance (ND), is common in inter- speci?c hybrids. (muni.cz)
  • We hypothesize that highly expressed variants with distinct IGS features may induce heritable epigenetic reprogramming of the partner rDNA arrays, harmonizing the expression of thousands of genes in allopolyploids. (muni.cz)
  • Such is the case with the rDNA locus, a relatively understudied and unusual form of heterochromatin consisting of tandemly repeated rRNA genes. (hhs.gov)
  • The methylation pattern within a specific multigene locus is influenced by the number and type of rRNA genes in other rDNA loci in the cell. (ncsu.edu)
  • In these cellular models, prolonged JHDM1B downregulation triggered a surge of 45S pre-rRNA transcription and processing, associated with a re-modulation of the H3K36me2 levels at rDNA loci and with changes in DNA methylation of specific CpG sites in rDNA genes. (oncotarget.com)
  • Moreover, the transferred gene has physically replaced the native rpl36 gene, yet flanking genes and intergenic regions show no sign of HGT. (biomedcentral.com)
  • In addition, IGS sequencing (e.g., sequencing of intergenic regions between the 16S and 23S rRNA genes) has been used to taxonomy studies, while partial sequencing of the gene gtfB , which encodes the enzyme glucosyltransferase B, has been used to investigate enzymatic activity and virulence 11-12 . (bvsalud.org)
  • A panel of 15 Mycobacterium marinum isolates was characterized by biochemical tests, sequencing the ribosomal DNA intergenic spacer (ITS) region and the heat shock protein 65 gene (hsp65) and pulsed-field gel electrophoresis (PFGE). (oregonstate.edu)
  • Transcription of the rDNA occurs in the FC. (wikipedia.org)
  • Paradoxically, the rDNA is heavily transcribed by RNA polymerase I (Pol I) to synthesize ribosomal RNA, yet retains several key heterochromatin characteristics such as suppression of recombination and "silencing" of RNA polymerase II (Pol II)-dependent transcription. (hhs.gov)
  • In budding yeast rDNA, transcription of non-coding RNAs from the intergenic spacers must be silenced by the conserved NAD+-dependent histone deacetylase Sir2 to maintain rDNA stability and support replicative lifespan. (hhs.gov)
  • As inferred from mouse cell models, intergenic spacer regions (IGS) located between rRNA transcription units contain upstream promoters and are transcribed by RNA Polymerase I. The IGS transcripts originate approximately 2 Kb upstream of the start of rRNA transcription and proceed though the main promoter of the rRNA gene. (reactome.org)
  • We observed that decapping mutants exhibit low levels of Sir2, which reduces silencing and leads to the elevated transcription of rDNA intergenic spacer regions. (uniroma1.it)
  • Intergenic transcription, particularly within repetitive DNA loci, can be deleterious. (mcgill-cihr-ig.ca)
  • The NAD-dependent histone deacetylase Sir2 controls ribosomal DNA (rDNA) silencing by inhibiting recombination and RNA polymerase II-catalyzed transcription in the rDNA of Saccharomyces cerevisiae Sir2 is recruited to nontranscribed spacer 1 (NTS1) of the rDNA array by interaction between the RENT ( RE: gulation of N: ucleolar S: ilencing and T: elophase exit) complex and the replication terminator protein Fob1. (omicsdi.org)
  • Sir2 is a component of the RENT complex, and its loading not only silences intrachromatid recombination in rDNA but also RNA polymerase II-catalyzed transcription. (omicsdi.org)
  • It is concluded that cytosine methylation in rDNA is regulated and that the methylation pattern correlates with the transcription potential of an rRNA gene. (ncsu.edu)
  • Here we explored the JmjC domain-containing histone demethylase 1B (JHDM1B) function in the epigenetic control of rDNA transcription. (oncotarget.com)
  • Chromatin immunoprecipitation (ChIP) showed that pS2 and another active form of Pol II, phosphorylated on serine 5 (pS5), were enriched across rDNA, with the highest levels-at IGS28 and IGS38-being comparable to those at known Pol-II-transcribed loci (Fig. 1b and Extended Data Fig. 1a, d-f ). (nature.com)
  • The observed low level of Sir2 may affect histone modification and induce loss of silencing at specific loci, as well as recombination within rDNA repeats, both of which have been shown to regulate cellular lifespan. (uniroma1.it)
  • The identification of species was addressed through a combination of biochemical and genetic methods (API ® 50 CHL test, 16S rDNA and recA gene sequences, Amplified Ribosomal DNA Restriction Analysis -ARDRA- and 16S-26S intergenic region analysis). (mdpi.com)
  • Sequencing of DNA fragments amplified from the 16S-23S rRNA intergenic spacer region and areas flanking the 23S rRNA gene grouped these isolates within the species Lactobacillus plantarum. (sun.ac.za)
  • The DNA quantity and purity were determined using real-time PCR targeting the bacterial 16S rDNA gene. (knaw.nl)
  • El an lisis se hizo por la reacci n en cadena de la polimerasa (PCR) y por secuenciaci n del DNA de la region correspondiente al gene rpo T de M. leprae . (ilsl.br)
  • Los aislados se clasificaron en dos grupos con base en el n mero de 'secuencias tandem' compuestas por 6 pares de bases en el gene rpo T. Los aislados de Jap n (excepto Okinawa) y Korea correspondieron a un genotipo, mientras que los aislados de los pa ses del sudeste asi tico, Brazil, Haiti, y Okinawa en Japon, correspondieron a un segundo genotipo. (ilsl.br)
  • An isolated bacterium TBE-8, was identified as Leuconostoc mesenteroides according to the sequences of 16S rDNA and the 16S-23S rDNA intergenic spacer region. (bvsalud.org)
  • The results are discussed in terms of a model in which repeated sequences in the wheat intergenic DNA are presumed to function as upstream promoters and transcriptional enhancers similar to those in Xenopus. (ncsu.edu)
  • Its flagellin and 16S rRNA central Europe, we screened questing ticks for 16S rDNA sequences resemble those of the relapsing fever spirochetes similar to that of Asian and American relapsing fever-like more closely than those of any of the known Lyme disease spirochetes. (cdc.gov)
  • Methods: S. mutans samples were isolated from the saliva of 30 children with varying histories of dental caries, and they were characterized according to morphological and biochemical markers and the sequences of their 16S-23S intergenic spacer region. (bvsalud.org)
  • The yeast Ataxin-2 protein Pbp1 binds intergenic RNA, represses RNA:DNA hybrids, and prevents aberrant rDNA recombination/replication. (mcgill-cihr-ig.ca)
  • This work provides new mechanistic insights into the regulation of rDNA silencing and intrachromatid recombination by showing that Sir2 recruitment is stringently regulated by Fob1 phosphorylation at specific sites in its C-terminal domain (C-Fob1), which also regulates long-range Ter-Ter interactions. (omicsdi.org)
  • Here, we show that the replication terminator protein Fob1 of Saccharomyces cerevisiae promoted chromosome kissing that initiated rDNA recombination and controlled the replicative life span (RLS). (omicsdi.org)
  • Oligomerization of Fob1 caused synaptic (kissing) interactions between pairs of terminator (Ter) sites that initiated recombination in rDNA. (omicsdi.org)
  • Consistent with this notion, stability of the ribosomal DNA (rDNA) repeats of budding yeast requires processes that counteract RNA polymerase II (RNAPII) function at intergenic spacers within the repeats. (mcgill-cihr-ig.ca)
  • Les isolats furent class s en deux groupes bas s sur le nombre de motifs r p t s 2 par 2 (tandem repeats) compos s de 6 paires de bases au sein du g ne rpoT. (ilsl.br)
  • In yeast, the 5S rDNA sequence is localized in the intergenic spacer and is transcribed in the nucleolus by RNA pol. (wikipedia.org)
  • We anticipate these studies in yeast will provide a paradigm for future structural-function studies of rDNA heterochromatin during aging in mammalian cells. (hhs.gov)
  • The shield prevents Pol I from producing sense intergenic noncoding RNAs (sincRNAs) that can disrupt nucleolar organization and rRNA expression. (nature.com)
  • PCR for the 5S rDNA intergenic spacer region and a multiplex PCR, followed by sequencing identified the parasite as Trichinella papuae . (cdc.gov)
  • Reflecting the substantial increase in the DNA intergenic region, an original fibrillar component would have separated into the FC and the DFC. (wikipedia.org)
  • 1997. An AluI fragment isolated from lake trout (Salvelinus namaycush), maps to the intergenic spacer region of the rDNA cistron . (ucsb.edu)
  • The replication terminator protein Fob1 of Saccharomyces cerevisiae is multifunctional, and it not only promotes polar replication fork arrest at the tandem Ter sites located in the intergenic spacer region of rDNA but also loads the NAD-dependent histone deacetylase Sir2 at Ter sites via a protein complex called RENT (regulator of nucleolar silencing and telophase exit). (omicsdi.org)
  • In addition, we have mapped several DNase I-hypersensitive sites in the intergenic spacer region of the rDNA repeating unit. (ncsu.edu)
  • In general, for unknown molds, the ITS region of the rDNA is used as the primary target with primers ITS-1 and ITS-4 as the most general primer set. (cdc.gov)
  • For identification of Trichosporon species, the intergenic region of the ribosomal cistron is used (Sugita, 2002). (cdc.gov)
  • The ribosomal PCR product of some of the phytoplasmas was cloned and the l6S/23S intergenic spacer region was sequenced to identify more subtle differences in the SPLL-type phytoplasmas. (edu.au)
  • In some of the phytoplasmas some minor nucleotide changes were identified in the variable regions of the spacer region either side of the conserved tRNAIle. (edu.au)
  • By sequencing the 16S-23S intergenic region, it was found that all of the isolates belonged to the species S. mutans . (bvsalud.org)
  • The experiments in this project are designed to identify determine how stabilization of the rDNA array by SIR2 and cohesin leads to improved fidelity of chromosome segregation. (hhs.gov)
  • We report a process of rDNA repeat stabilization that relies on suppressing intergenic RNA:DNA hybrids. (mcgill-cihr-ig.ca)
  • Despite preserved intergenic spacer (IGS) structure, they showed altered cytosine methylation and chromatin condensation patterns, and a correlation between expression, hypomethylation of RNA Pol I promoters and chromatin decondensation was apparent. (muni.cz)
  • La r action de polymerase en chain (PCR) suivie par le s quen age des produits obtenus fut r alis e sur le g ne rpoT de M. leprae . (ilsl.br)
  • These primers amplify a section of the intergenic spacer in the ribosomal cistron. (cdc.gov)
  • To examine the molecular basis of such variation, we studied the genetic and epigenetic features of rDNA homeologs in several lines derived from recently and independently formed natural populations. (muni.cz)
  • Among P. rubens individuals threefold variation was observed in the rDNA copy concentration, and among P. mariana individuals such variation was as much as sixfold. (lookformedical.com)
  • Original p-rDNA dominance was not restored in later generations, even in those segregants that inherited the corresponding parental rDNA genotype, thus indicating the generation of additional p-rDNA and d-rDNA epigenetic variants. (muni.cz)
  • We have previously shown that these and other examples of nucleolar dominance in wheat are associated with undermethylation of cytosine residues in certain regions of the dominant rDNA. (ncsu.edu)
  • Interestingly, the replicatively aging cells also have a chromosome instability (CIN) phenotype that is driven by the rDNA instability. (hhs.gov)
  • In Saccharomyces cerevisiae, 100-200 copies of a 9.1-kb rDNA repeat exist as a tandem array on chromosome XII. (omicsdi.org)
  • Overexpression of the Mcd1 subunit of cohesin suppresses the age-induced rDNA and CIN phenotypes, and strongly extends lifespan. (hhs.gov)
  • In addition, Pbp1 suppresses hybrids at specific non-rDNA sites. (mcgill-cihr-ig.ca)
  • Interpopulation crosses between progenitors display- ing reciprocal ND resulted in d-rDNA dominance, indicating immediate suppression of p-homeologs in F 1 hybrids. (muni.cz)
  • Targeted elimination of RNA:DNA hybrids via various methods restores rDNA stability in Pbp1-deficient cells. (mcgill-cihr-ig.ca)
  • Replication fork arrest and rDNA silencing are two independent and separable functions of the replication terminator protein Fob1 of Saccharomyces cerevisiae. (omicsdi.org)
  • Heterochromatin consists of large domains of repetitive DNA such as centromeres, telomeres, rDNA, and retrotransposons that remain organized into compact chromatin structures throughout interphase, when other portions of the chromosomes (euchromatin) usually decondense. (hhs.gov)
  • We hypothesize that rDNA interactions with the genome, including centromeres, play a significant role in the age-induced CIN phenotype. (hhs.gov)
  • Therefore, we will develop a method to define genome-wide rDNA contacts, and test how these contacts change with age or when rRNA synthesis is compromised. (hhs.gov)
  • At a size greater than 32 kbp and at a concentration averaging 1.2-1.3 x 10(4) copies/pg, the rDNA constitutes approximately 4% of the total genome. (lookformedical.com)
  • Assessment Of The Genetic Diversity Of Xylella Fastidiosa Isolated From Citrus In Brazil By Pcr-rflp Of The 16s Rdna And 16s-23s Intergenic Spacer And Rep-pcr Fingerprinting . (uchile.cl)
  • Inbred lines derived from T. mirus with a dominant d-rDNA homeolog transmitted this expression pattern over generations, which may explain why it is prevalent among natural populations. (muni.cz)
  • In contrast, lines derived from the p-rDNA dominant progenitor were meioti- cally unstable, frequently switching to co-dominance. (muni.cz)
  • Sequence analysis of 16S rDNA showed that AGY clustered with the aster yellows group and was most closely related to, but not the same as, the stolbur subgroup, forming a new subgroup. (edu.au)
  • In eukaryotic cells, ribosomal DNA (rDNA) forms the basis of the nucleolus. (omicsdi.org)
  • First, a Fob1 ortholog of Saccharomyces bayanus expressed in a fob1Delta strain of S. cerevisiae restored polar fork arrest at Ter but not rDNA silencing. (omicsdi.org)
  • Microbial community fingerprints were assessed by automated ribosomal intergenic spacer analysis. (knaw.nl)
  • By applying Automated ribosomal RNA intergenic spacer analysis (ARISA), PHYLOCHHIP - analysis and sequencing of 18S rDNA clone librarieson on the gut content of two Southern Ocean salps, Salpa thompsoni and Ihlea racovitzai from various season of the Lazarev sea, we will investigate the seasonality and spatial variablility of phytoplankton. (uni-rostock.de)
  • Restriction fragment length polymorphisms (RFLP) analysis of 16S rDNA showed that AGY was different to other characterised phytoplasmas occurring in grapevine, and most closely resembled stolbur phytoplasmas associated with bois noir from France and Vergilbungskrankheit from Germany. (edu.au)
  • however, at position 5 of the ITS rDNA, a single nucleotide polymorphism was identified. (oregonstate.edu)
  • Slot-blot hybridizations were used to determine the nuclear rDNA copy concentration. (lookformedical.com)
  • This results in deterioration of the rDNA heterochromatin and instability of the array. (hhs.gov)
  • Second, a mutant form (I407T) of S. cerevisiae Fob1 retained normal fork arresting activity but was partially defective in rDNA silencing. (omicsdi.org)