The nucleolus and transcription of ribosomal genes

Raška, Ivan; Koberna, Karel; Malínský, J; Fidlerová, Helena; Mašata, Martin

doi:10.1016/j.biolcel.2004.04.015

Cited by 125 publications

(127 citation statements)

References 165 publications

(271 reference statements)

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“…Several growth dependant signaling pathways have been implicated in regulating rRNA levels [13], such as the mammalian target of rapamycin (mTOR) and mitogen activated protein kinase (MAPK) pathways, both of which have been described as crucial for melanoma activation and progression [14;15]. Thus, as with GAPDH, it is understandable as to why 18S rRNA is not a good choice as a control gene for melanoma and normal tissue types.…”

Section: Expression Of 18s Rrna and Gapdhmentioning

confidence: 99%

The normalization of gene expression data in melanoma: Investigating the use of glyceraldehyde 3-phosphate dehydrogenase and 18S ribosomal RNA as internal reference genes for quantitative real-time PCR

Giricz

Lauer‐Fields

Fields

2008

Analytical Biochemistry

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We examined a panel of 26 melanoma and fibroblast samples (tissues and cultured cells) to evaluate the suitability of two commonly used housekeeping genes, GAPDH and 18S rRNA, for quantitative real-time PCR. Both genes showed significant variations within the individual cell line and tissue groups. While no overall trends were observed in the expression of the 18S rRNA, GAPDH was upregulated in melanoma tissue and cultured cells compared to the corresponding normal samples. In melanoma and fibroblast cell lines and tissues, absolute quantification appears to be more appropriate than normalizing mRNA expression via GAPDH or 18S rRNA housekeeping genes.The number of skin cancer cases has been steadily increasing with the risk of developing malignant cutaneous melanoma doubling every 10-15 years [1]. However, in 2007 the new cases of melanoma was estimated at 59,940, nearly double that of previous estimates [2]. If melanoma is detected early (localized), the five year survival rate is ∼99% [3]. However, distant stage (metastatic) melanoma has a very poor prognosis (∼15% five year survival) [3]. Thus, there is a critical requirement for accurate assessment of melanoma initiation and progression, as well as the characterization of the more malignant later stages.The most reliable prognostic factor of melanoma is still the tumor thickness [4], thus underscoring the importance of early detection and surgery. Better knowledge of the underlying molecular mechanisms of transformation and melanoma progression would possibly aid in the discovery of novel biomarkers, potential therapeutic targets, or biochemical pathways. Previous studies have shown that gene expression profiling of melanoma mRNA levels may lead to novel molecular classification methods by identifying the subtypes of disease and possibly predicting phenotypic characteristics ([5] and references cited therein). Microarray analysis can be used for the high-throughput analysis of global gene expression levels, studying hundreds or thousands of targets at once. Quantitative real-time PCR (qRT-PCR or qPCR) allows for the sensitivity to analyze a narrow range of targets or to confirm previously obtained microarray data.Currently there are two quantification methods available for qPCR, absolute and relative. In the case of absolute quantification, genomic DNA or plasmids containing cloned qPCR target *Corresponding author. Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991, USA. Tel: 1-561-297-2093. Fax: 1-561-297-2759. E-mail address: fieldsg@fau.edu. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal di...

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Section: Expression Of 18s Rrna and Gapdhmentioning

confidence: 99%

The normalization of gene expression data in melanoma: Investigating the use of glyceraldehyde 3-phosphate dehydrogenase and 18S ribosomal RNA as internal reference genes for quantitative real-time PCR

Giricz

Lauer‐Fields

Fields

2008

Analytical Biochemistry

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“…Electron microscopic imaging of nucleoli reveal three distinct subcompartments: the fibrillar centers (FC), dense fibrillar components (DFC), and granular components (GC; Huang, 2002). It is at the FC/DFC border that RNA polymerase I (pol I) and other pol I-specific transcription factors associate to form the pol I preinitiation complex (PIC) at rRNA promoters (Grummt, 2003;Grummt and Pikaard, 2003) for transcription of rDNA (Raska et al, 2004). In vivo activation of the human rRNA promoter requires proteinprotein interactions between the DNA-binding protein, upstream binding factor (UBF1), and SL1 for the targeting of pol I and stable PIC formation (Bell et al, 1988;Friedrich et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Pol I Transcription and Pre-rRNA Processing Are Coordinated in a Transcription-dependent Manner in Mammalian Cells

Kopp

Gasiorowski

Chen

et al. 2007

MBoC

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Pre-rRNA synthesis and processing are key steps in ribosome biogenesis. Although recent evidence in yeast suggests that these two processes are coupled, the nature of their association is unclear. In this report, we analyze the coordination between rDNA transcription and pre-rRNA processing in mammalian cells. We found that pol I transcription factor UBF interacts with pre-rRNA processing factors as analyzed by immunoprecipitations, and the association depends on active rRNA synthesis. In addition, injections of plasmids containing the human rDNA promoter and varying lengths of 18S rDNA into HeLa nuclei show that pol I transcription machinery can be recruited to rDNA promoters regardless of the product that is transcribed, whereas subgroups of pre-rRNA processing factors are recruited to plasmids only when specific pre-rRNA fragments are produced. Our observations suggest a model for sequential recruitment of pol I transcription factors and pre-rRNA processing factors to elongating pre-rRNA on an as-needed basis rather than corecruitment to sites of active transcription. INTRODUCTIONNucleoli contain hundreds of tandem rRNA genes and a large number of factors necessary for transcription of ribosomal DNA (rDNA), processing of pre-rRNA, and ribosome assembly. Electron microscopic imaging of nucleoli reveal three distinct subcompartments: the fibrillar centers (FC), dense fibrillar components (DFC), and granular components (GC;Huang, 2002). It is at the FC/DFC border that RNA polymerase I (pol I) and other pol I-specific transcription factors associate to form the pol I preinitiation complex (PIC) at rRNA promoters (Grummt, 2003;Grummt and Pikaard, 2003) for transcription of rDNA (Raska et al., 2004). In vivo activation of the human rRNA promoter requires proteinprotein interactions between the DNA-binding protein, upstream binding factor (UBF1), and SL1 for the targeting of pol I and stable PIC formation (Bell et al., 1988;Friedrich et al., 2005). In combination with several other evolutionarily conserved proteins, these and other pol I transcription factors confer pol I promoter specificity to produce a single polycistronic pre-rRNA transcript (45S pre-rRNA in humans; Grummt, 2003;Grummt and Pikaard, 2003).A large number of small nucleolar ribonucleoproteins (snoRNPs), composed of small nucleolar RNAs (snoRNAs) and their associated proteins, as well as more than 100 protein cofactors, are responsible for processing the 45S transcript (Fromont-Racine et al., 2003;Granneman and Baserga, 2005). The box C/D snoRNA U3 and its associated proteins are required for the initial cleavages of the 5Ј end of pre-rRNA at sites A 0 , A 1 , and A 2 and are thereby involved in the release of the 18S precursor (Fromont-Racine et al., 2003;Granneman and Baserga, 2005). Yeast U3 snoRNA exists in at least two types of complexes in vitro: a 12S monoparticle (Billy et al., 2000;Granneman et al., 2003) and a larger ϳ90S complex termed the small subunit (SSU) processome (Fabrizio et al., 1994;Dragon et al., 2002). The 12S monoparticle pre...

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“…In actively growing animal and plant cells, rRNA synthesis accounts for about 50 -80% of total cellular RNA production (1). Human diploid cells contain about 400 ribosomal genes organized as tandem repeats at nucleolus organizer regions encoded on chromosomes 13, 14, 15, 21, and 22 (1,2).…”

mentioning

confidence: 99%

Microspherule Protein 1, Mi-2β, and RET Finger Protein Associate in the Nucleolus and Up-regulate Ribosomal Gene Transcription

Shimono

Shimokata

et al. 2005

Journal of Biological Chemistry

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The nucleolus is the site of ribosomal DNA (rDNA) transcription and ribosome production. In exploring the role of nucleolar protein MCRS1 (microspherule protein1)/MSP58 (58-kDa microspherule protein), we found that Mi-2␤, a component of a nucleosome remodeling and deacetylase (NuRD) complex, RET finger protein (RFP), and upstream binding factor (UBF) were associated with MCRS1. Yeast two-hybrid assays revealed that MCRS1 bound to the ATPase/helicase region of Mi-2␤ and the coiled-coil region of RFP. Interestingly, confocal microscopic analyses revealed the co-localization of MCRS1, Mi-2␤, RFP, and the rRNA transcription factor UBF in the nucleoli. We also found that MCRS1, Mi-2␤, and RFP were associated with rDNA using a chromatin immunoprecipitation assay. Finally, we showed that MCRS1, Mi-2␤, and RFP up-regulated transcriptional activity of the rDNA promoter and that ribosomal RNA transcription was repressed when MCRS1, Mi-2␤, and RFP expression was reduced using siRNA. These results indicated that Mi-2␤ and RFP, known to be involved in transcriptional repression in the nucleus, co-localize with MCRS1 in the nucleolus and appear to activate the rRNA transcription.

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The nucleolus and transcription of ribosomal genes

Cited by 125 publications

References 165 publications

The normalization of gene expression data in melanoma: Investigating the use of glyceraldehyde 3-phosphate dehydrogenase and 18S ribosomal RNA as internal reference genes for quantitative real-time PCR

The normalization of gene expression data in melanoma: Investigating the use of glyceraldehyde 3-phosphate dehydrogenase and 18S ribosomal RNA as internal reference genes for quantitative real-time PCR

Pol I Transcription and Pre-rRNA Processing Are Coordinated in a Transcription-dependent Manner in Mammalian Cells

Microspherule Protein 1, Mi-2β, and RET Finger Protein Associate in the Nucleolus and Up-regulate Ribosomal Gene Transcription

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