Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
BMC Evol Biol
2005 Feb 13;5:15. doi: 10.1186/1471-2148-5-15.
Show Gene links
Show Anatomy links
The architecture of mammalian ribosomal protein promoters.
Perry RP
.
???displayArticle.abstract???
BACKGROUND: Mammalian ribosomes contain 79 different proteins encoded by widely scattered single copy genes. Coordinate expression of these genes at transcriptional and post-transcriptional levels is required to ensure a roughly equimolar accumulation of ribosomal proteins. To date, detailed studies of only a very few ribosomal protein (rp) promoters have been made. To elucidate the general features of rp promoter architecture, I made a detailed sequence comparison of the promoter regions of the entire set of orthologous human and mouse rp genes.
RESULTS: A striking evolutionarily conserved feature of most rp genes is the separation by an intron of the sequences involved in transcriptional and translational regulation from the sequences with protein encoding function. Another conserved feature is the polypyrimidine initiator, which conforms to the consensus (Y)2C+1TY(T)2(Y)3. At least 60 % of the rp promoters contain a largely conserved TATA box or A/T-rich motif, which should theoretically have TBP-binding capability. A remarkably high proportion of the promoters contain conserved binding sites for transcription factors that were previously implicated in rp gene expression, namely upstream GABP and Sp1 sites and downstream YY1 sites. Over 80 % of human and mouse rp genes contain a transposable element residue within 900 bp of 5' flanking sequence; very little sequence identity between human and mouse orthologues was evident more than 200 bp upstream of the transcriptional start point.
CONCLUSIONS: This analysis has provided some valuable insights into the general architecture of mammalian rp promoters and has identified parameters that might coordinately regulate the transcriptional activity of certain subsets of rp genes.
Figure 1. The location of insertion elements in the 5'-flanking regions of rp genes. Insertion (ins) elements were identified by the RepeatMasker program in scans of up to one kilobase of sequence 5' of the tsp, and the location of the element nearest to the tsp recorded for 79 human and mouse rp genes [see Additional file 2]. The distance from the tsp was divided into 200 bp intervals, the percentage of rp genes with an element within each interval determined, and the values plotted cumulatively against the distance from the tsp.
Figure 2. Criteria for rp promoter annotation. (a). Quality of the TATA box for TBP binding based on a structural analysis of TBP-DNA complexes. Rules adopted for + and +/- ranking and some examples in rp promoters are shown at the right. (b). Criteria used for identification of potential transcription factor-binding sites by the rVISTA program for motifs aligned in human-mouse promoter sequence comparisons and with the FindPatterns program for unaligned motifs.
Figure 3. Examples of comparisons of human and mouse rp promoter sequences from -200 to +100. Exon I is in uppercase letters, highlighted in yellow with the ATG translation initiation codon, if present, highlighted in gray. The sequences evaluated for TATA box quality are highlighted in green. Putative transcription factor-binding sites in aligned sequences are shown above the sequences, highlighted in fuchsia; sites in unaligned sequences are shown above the human or below the mouse sequences and enclosed in carets. An upstream sequence identified as an insertion element is in red letters. Gaps inserted by the alignment program to maximize overall sequence identity are indicated by dashes. (a) rpS18 , (b) rpL30 , (c) rpS4 , (d) rpL13a . In rpL30 the elements with known functional relevance are underlined with asterisks.
Figure 4. The consensus initiator sequence of mammalian rp genes. Seventy-nine pairs of orthologous human and mouse rp gene sequences were compared at positions -8 to +10 and the occurrence of each nucleotide or pair of nucleotides depicted by the height of the letters: A, G, C. T, Y = C/T, R = A/G, W = A/T, K = G/T, S = C/G, M = C/A. The tsp is the C at position +1.
Figure 5. Comparison of rpS3 promoter sequences in human (Hs), mouse (Mm), Xenopus laevis (Xl) and Fugu rubripes (Fr). Alignment by the ClustalW program with 100% and 75% identities enclosed in boxes. The first exon is highlighted in yellow with the ATG translation initiation codon in gray. Putative binding sites for TBP, GABP, Sp1 and YY1 are highlighted in green, red, blue and pink, respectively.
Figure 6. Classification of rp gene promoters. The data in Table 1 were used to classify the rp promoters into eight groups according to whether they contain aligned sites for GABP, Sp1, YY1, or various combinations of these factors. The promoters highlighted in green are those in which the TATA box quality of both orthologues was ranked as + or in which one ranked as + and the other as +/-. The promoters highlighted in yellow are those in which both orthologues ranked as +/- or in which one ranked as + and the other as -. Non highlighted promoters are those in which both orthologues ranked as – or in which one ranked as +/- and the other as -.
Antoine,
Functional characterization of transcriptional regulatory elements in the upstream region and intron 1 of the human S6 ribosomal protein gene.
1998, Pubmed
Antoine,
Functional characterization of transcriptional regulatory elements in the upstream region and intron 1 of the human S6 ribosomal protein gene.
1998,
Pubmed
Batchelor,
The structure of GABPalpha/beta: an ETS domain- ankyrin repeat heterodimer bound to DNA.
1998,
Pubmed
Bray,
AVID: A global alignment program.
2003,
Pubmed
Chung,
Cell-free transcription of a mouse ribosomal-protein-encoding gene: the effects of promoter mutations.
1991,
Pubmed
Chung,
The importance of downstream delta-factor binding elements for the activity of the rpL32 promoter.
1993,
Pubmed
Colombo,
Functional elements of the ribosomal protein L7a (rpL7a) gene promoter region and their conservation between mammals and birds.
1992,
Pubmed
Curcić,
GA-binding protein is involved in altered expression of ribosomal protein L32 gene.
1997,
Pubmed
Davies,
The L19 ribosomal protein gene (RPL19): gene organization, chromosomal mapping, and novel promoter region.
1995,
Pubmed
De Rinaldis,
The binding sites for Xenopus laevis FIII/YY1 in the first exon of L1 and L14 ribosomal protein genes are dispensable for promoter expression.
1998,
Pubmed
,
Xenbase
Dermitzakis,
Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover.
2002,
Pubmed
Dudov,
The gene family encoding the mouse ribosomal protein L32 contains a uniquely expressed intron-containing gene and an unmutated processed gene.
1984,
Pubmed
Duret,
Searching for regulatory elements in human noncoding sequences.
1997,
Pubmed
Genuario,
Comparative utilization of transcription factor GABP by the promoters of ribosomal protein genes rpL30 and rpL32.
1993,
Pubmed
Genuario,
The GA-binding protein can serve as both an activator and repressor of ribosomal protein gene transcription.
1996,
Pubmed
Gerbasi,
Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression.
2004,
Pubmed
Hariharan,
A characterization of the elements comprising the promoter of the mouse ribosomal protein gene RPS16.
1989,
Pubmed
Hariharan,
Equipotent mouse ribosomal protein promoters have a similar architecture that includes internal sequence elements.
1989,
Pubmed
Hariharan,
Functional dissection of a mouse ribosomal protein promoter: significance of the polypyrimidine initiator and an element in the TATA-box region.
1990,
Pubmed
Harris,
Comparison of the mouse L32 ribosomal protein promoter elements in mouse myoblasts, fibers, and L cells.
1992,
Pubmed
Higa,
Gene organization and sequence of the region containing the ribosomal protein genes RPL13A and RPS11 in the human genome and conserved features in the mouse genome.
1999,
Pubmed
Kato,
Construction of a human full-length cDNA bank.
1994,
Pubmed
Kirn-Safran,
Cloning, expression, and chromosome mapping of the murine Hip/Rpl29 gene.
2000,
Pubmed
Levy,
Oligopyrimidine tract at the 5' end of mammalian ribosomal protein mRNAs is required for their translational control.
1991,
Pubmed
Loots,
rVista for comparative sequence-based discovery of functional transcription factor binding sites.
2002,
Pubmed
Marchioni,
XrpFI, an amphibian transcription factor composed of multiple polypeptides immunologically related to the GA-binding protein alpha and beta subunits, is differentially expressed during Xenopus laevis development.
1993,
Pubmed
,
Xenbase
Mayor,
VISTA : visualizing global DNA sequence alignments of arbitrary length.
2000,
Pubmed
Meyuhas,
Synthesis of the translational apparatus is regulated at the translational level.
2000,
Pubmed
Meyuhas,
Construction and identification of cDNA clones for mouse ribosomal proteins: application for the study of r-protein gene expression.
1980,
Pubmed
Meyuhas,
The mouse ribosomal protein L7 gene. Its primary structure and functional analysis of the promoter region.
1990,
Pubmed
Moura-Neto,
An element downstream of the cap site is required for transcription of the gene encoding mouse ribosomal protein L32.
1989,
Pubmed
Overman,
Multiple regulatory elements ensure accurate transcription of a human ribosomal protein gene.
1993,
Pubmed
Pata,
Structural characterization of the mouse ribosomal protein S6-encoding gene.
1996,
Pubmed
Patikoglou,
TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.
1999,
Pubmed
Rebane,
A novel snoRNA (U73) is encoded within the introns of the human and mouse ribosomal protein S3a genes.
1998,
Pubmed
Rezai-Zadeh,
Targeted recruitment of a histone H4-specific methyltransferase by the transcription factor YY1.
2003,
Pubmed
Shi,
Everything you have ever wanted to know about Yin Yang 1.....
1997,
Pubmed
Smale,
The RNA polymerase II core promoter.
2003,
Pubmed
Sugahara,
Comparative evaluation of 5'-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries.
2001,
Pubmed
Sáfrány,
The relative contributions of various transcription factors to the overall promoter strength of the mouse ribosomal protein L30 gene.
1995,
Pubmed
Thomas,
Unlocking the mechanisms of transcription factor YY1: are chromatin modifying enzymes the key?
1999,
Pubmed
Thompson,
Convergence of Ets- and notch-related structural motifs in a heteromeric DNA binding complex.
1991,
Pubmed
Uechi,
A complete map of the human ribosomal protein genes: assignment of 80 genes to the cytogenetic map and implications for human disorders.
2001,
Pubmed
Wagner,
Characterization of the multigene family encoding the mouse S16 ribosomal protein: strategy for distinguishing an expressed gene from its processed pseudogene counterparts by an analysis of total genomic DNA.
1985,
Pubmed
Wiedemann,
Characterization of the expressed gene and several processed pseudogenes for the mouse ribosomal protein L30 gene family.
1984,
Pubmed
Wiley,
Functional binding of the "TATA" box binding component of transcription factor TFIID to the -30 region of TATA-less promoters.
1992,
Pubmed
Wool,
Extraribosomal functions of ribosomal proteins.
1996,
Pubmed
Yoganathan,
A positive regulator of the ribosomal protein gene, beta factor, belongs to the ETS oncoprotein family.
1992,
Pubmed
Yoganathan,
Direct binding of yeast transcription factor (TFIID) to the ribosomal protein L32 (rpL32) TATA-less promoter sequence.
1993,
Pubmed
Yoshihama,
The human ribosomal protein genes: sequencing and comparative analysis of 73 genes.
2002,
Pubmed
Zhang,
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome.
2002,
Pubmed
Zimmermann,
The double life of ribosomal proteins.
2003,
Pubmed
Zinn,
Structure and function of ribosomal protein S4 genes on the human and mouse sex chromosomes.
1994,
Pubmed
