Ribosomal protein L7a is encoded by a gene (Surf-3) within the tightly clustered mouse surfeit locus

Preservation of ranking order in the expression of human Housekeeping genes

Housekeeping (HK) genes fulfill the basic needs for a cell to survive and function properly. Their ubiquitous expression, originally thought to be constant, can vary from tissue to tissue, but this variation remains largely uncharacterized and it could not be explained by previously identified properties of HK genes such as short gene length and high GC content. By analyzing microarray expression data for human genes, we uncovered a previously unnoted characteristic of HK gene expression, namely that the ranking order of their expression levels tends to be preserved from one tissue to another. Further analysis by tensor product decomposition and pathway stratification identified three main factors of the observed ranking preservation, namely that, compared to those of non-HK (NHK) genes, the expression levels of HK genes show a greater degree of dispersion (less overlap), stableness (a smaller variation in expression between tissues), and correlation of expression. Our results shed light on regulatory mechanisms of HK gene expression that are probably different for different HK genes or pathways, but are consistent and coordinated in different tissues.

The origin of a developmentally regulated Igh replicon is located near the border of regulatory domains for Igh replication and expression

The 3' Ig heavy chain locus (Igh) regulatory region is the most downstream known element of the murine Igh gene cluster. We report here that the nearest non-Igh genes-Crip, Crp2, and Mta1-are located approximately 70 kb further downstream and are beyond the end of the domain of Igh transcriptional regulation. We have localized an origin of replication in MEL cells to a 3-kb segment located between the 3' Igh regulatory region and Crip. Sequences downstream of this origin are replicated by forks that move in both directions. Sequences upstream of this origin (Igh-C, -D, and -J) are replicated in a single direction through a 500-kb segment in which no active bidirectional origins can be detected. We propose that this origin may lie at or near the end of the Igh regulation domain.

Surfeit locus gene homologs are widely distributed in invertebrate genomes

The mouse Surfeit locus contains six sequence-unrelated genes (Surf-1 to -6) arranged in the tightest gene cluster so far described for mammals. The organization and juxtaposition of five of the Surfeit genes (Surf-1 to -5) are conserved between mammals and birds, and this may reflect a functional or regulatory requirement for the gene clustering. We have undertaken an evolutionary study to determine whether the Surfeit genes are conserved and clustered in invertebrate genomes. Drosophila melanogaster and Caenorhabditis elegans homologs of the mouse Surf-4 gene, which encodes an integral membrane protein associated with the endoplasmic reticulum, have been isolated. The amino acid sequences of the Drosophila and C. elegans homologs are highly conserved in comparison with the mouse Surf-4 protein. In particular, a dilysine motif implicated in endoplasmic reticulum localization of the mouse protein is conserved in the invertebrate homologs. We show that the Drosophila Surf-4 gene, which is transcribed from a TATA-less promoter, is not closely associated with other Drosophila Surfeit gene homologs but rather is located upstream from sequences encoding a homolog of a yeast seryl-tRNA synthetase protein. There are at least two closely linked Surf-3/rpL7a genes or highly polymorphic alleles of a single Surf-3/rpL7a gene in the C. elegans genome. The chromosomal locations of the C. elegans Surf-1, Surf-3/rpL7a, and Surf-4 genes have been determined. In D. melanogaster the Surf-3/rpL7a, Surf-4, and Surf-5 gene homologs and in C. elegans the Surf-1, Surf-3/rpL7a, Surf-4, and Surf-5 gene homologs are located on completely different chromosomes, suggesting that any requirement for the tight clustering of the genes in the Surfeit locus is restricted to vertebrate lineages.

A nuclear hormone receptor-associated protein that inhibits transactivation by the thyroid hormone and retinoic acid receptors

Nuclear hormone receptors are transcription factors that require multiple protein-protein interactions to regulate the expression of their target genes. Using the yeast two-hybrid system, we identified a protein, thyroid hormone receptor uncoupling protein (TRUP), that specifically interacts with a region of the human thyroid hormone receptor (TR) consisting of the hinge region and the N-terminal portion of the ligand binding domain in a hormone-independent manner. Interestingly, TRUP inhibits transactivation by TR and the retinoic acid receptor but has no effect on the estrogen receptor or the retinoid X receptor in mammalian cells. We also demonstrate that TRUP exerts its action on TR and retinoic acid receptor by interfering with their abilities to interact with their DNA. TRUP represents a type of regulatory protein that modulates the transcriptional activity of a subclass of the nuclear hormone receptor superfamily by preventing interaction with their genomic response elements.

The genomic organization of the region containing the Drosophila melanogaster rpL7a (Surf-3) gene differs from those of the mammalian and avian Surfeit loci

The Surf-3 gene of the unusually tight mouse Surfeit locus gene cluster has been identified as the highly conserved ribosomal protein gene L7a (rpL7a). The topography and juxtaposition of the Surfeit locus genes are conserved for the 600 million years of divergent evolution between mammals and birds. This suggests cis interaction and/or coregulation of the genes and suggests that, within this locus, gene organization plays an important role in gene expression. The further evolutionary conservation of the organization of the Surfeit locus was investigated. A cDNA encoding the Drosophila melanogaster homolog of the Surf-3/rpL7a gene was cloned, was shown to be present as a single copy, and was expressed constitutively at high levels throughout development. Genomic cosmid clones encompassing the gene and its surrounding DNA were isolated. The gene was determined to have five introns, of which two were located in the 5' untranslated region of the gene. The remaining three introns had splice sites at positions equivalent to those found in the Surf-3/rpL7a mammalian homologs. S1 analysis and 5' rapid amplification of cDNA ends both confirmed the start of transcription to occur in a polypyrimidine tract in the absence of a TATA box in the promoter. The genomic region around the Surf-3/rpL7a gene was analyzed by low-stringency hybridization with murine Surfeit gene probes, by partial sequence analysis, and by hybridization of fragments to Northern (RNA) blots. No homologs of other members of the Surfeit gene cluster were detected in close proximity to the D. melanogaster Surf-3/rpL7a gene. However, a gene which was detected directly 3' to the Surf-3/rpL7a gene was shown to encode a homolog of a mammalian serine-pyruvate aminotransferase.

Conservation of the organization of five tightly clustered genes over 600 million years of divergent evolution

The organization of the mouse surfeit locus is unusual in that it contains six housekeeping genes (Surf-1-Surf-6), which are unrelated by sequence homology, in the tightest mammalian gene cluster thus far described. A maximum of only 73 base pairs separates any two of the four well-characterized genes, and two of the genes overlap at their 3' ends. The direction of transcription of each of the five surfeit genes, Surf-1-Surf-5, alternates with respect to that of its neighbor, suggesting cis-interaction or coregulation between the genes by mechanisms such as the sharing of regulatory elements and/or antisense regulation. The Surf-3 gene has been identified as encoding the ribosomal protein L7a (Rpl7a). We have used the high conservation of the Rpl7a gene to clone the chicken gene and surrounding genomic DNA. The tight clustering and juxtaposition of at least five of the surfeit genes (Surf-1-Surf-5) and their associated CpG-rich islands have been found to be conserved over the 600 million years of divergent evolution that separates birds and mammals. This strongly suggests that the surfeit locus represents a different form of gene cluster in which gene organization may play both a positive and negative regulatory role in gene expression possibly via cis-interactions between the closely spaced genes.

Functional elements of the ribosomal protein L7a (rpL7a) gene promoter region and their conservation between mammals and birds

The transcriptional initiation sites of the chicken ribosomal protein L7a (rpL7a) gene have been determined and found to occur at three consecutive cytidine residues at the start of a polypyrimidine tract of 8 base pairs (bp). A comparative analysis of the 5' upstream regions of the mouse, human and chicken rpL7a genes identified two sequence elements (Box A and Box B) conserved over the 600 million years of divergent evolution that separate mammals and birds. Only Box A (nts - 56 to - 39) and Box B (nts - 25 to - 4) sequences were detected to bind nuclear factors from mouse nuclear extracts in an analysis of the mouse rpL7a 5' upstream sequence. Box A and Box B bind different nuclear factors and the factor binding to mouse Box A and mouse Box B sequences could be effectively competed by corresponding homologous sequences from the human and chicken rpL7a promoters. These results indicate that elements of the rpL7a promoter region are conserved between mammals and birds. An in vivo analysis of the mouse rpL7a 5' upstream sequence required for efficient transcription identified the 5' border of the minimal promoter region as lying between nts - 50 and - 56. Constructs containing 56 bp of 5' upstream DNA and the first 25 bp rpL7a exon were very efficiently transcribed indicating that sequences within the first intron are not required for gene expression. No sequence similarity was detected between the rpL7a promoter elements and described promoter elements of other eukaryotic ribosomal protein genes.

The mouse rpL7a gene is typical of other ribosomal protein genes in it's 5' region but differs in being located in a tight cluster of CpG-rich islands

The two major transcriptional start sites of the mouse ribosomal protein L7a gene (rpL7a) (formerly Surf-3) have been mapped to two cytidine residues separated by 4 bp embedded in a polypyrimidine tract of 21 bp. The rpL7a gene contains a small first exon (25-29 bp) and a small 5' untranslated leader sequence (22-26 bp). Its transcriptional start sites are not preceded by a canonical TATA box motif and its 5' end is located in a CpG-rich island. These are all features found associated with the five other functional mammalian ribosomal protein genes which have been previously characterized. The mouse rpL7a gene is found within a very tight cluster of six genes associated with 4 CpG-rich islands located in 32 kb of genomic DNA. Unique DNA probes located both upstream and downstream of the mouse rpL30 and rpL32 genes used on Southern blots of mouse DNA cleaved with a variety of CpG-rich island specific restriction enzymes did not detect CpG-rich islands in the close vicinity of these ribosomal protein genes. Thus the clustering of CpG-rich islands associated with rpL7a does not appear to be a general feature of mammalian ribosomal protein genes.

A human cellular sequence implicated in trk oncogene activation is DNA damage inducible

Xeroderma pigmentosum cells, which are deficient in the repair of UV light-induced DNA damage, have been used to clone DNA-damage-inducible transcripts in human cells. The cDNA clone designated pC-5 hybridizes on RNA gel blots to a 1-kilobase transcript, which is moderately abundant in nontreated cells and whose synthesis is enhanced in human cells following UV irradiation or treatment with several other DNA-damaging agents. UV-enhanced transcription of C-5 RNA is transient and occurs at lower fluences and to a greater extent in DNA-repair-deficient than in DNA-repair-proficient cells. Southern blot analysis indicates that the C-5 gene belongs to a multigene family. A cDNA clone containing the complete coding sequence of C-5 was isolated. Sequence analysis revealed that it is homologous to a human cellular sequence encoding the amino-terminal activating sequence of the trk-2h chimeric oncogene [Kozma, S. C., Redmond, S. M. S., Xiao-Chang, F., Saurer, S. M., Groner, B. & Hynes, N. E. (1988) EMBO J. 7, 147-154]. The presence of DNA-damage-responsive sequences at the 5' end of a chimeric oncogene could result in enhanced expression of the oncogene in response to carcinogens.

Ribosomal protein L4 of Saccharomyces cerevisiae: the gene and its protein

The sequence of a gene for ribosomal protein L4 of Saccharomyces cerevisiae has been determined. Unlike most ribosomal protein genes of S. cerevisiae this gene has no intron. The single open reading frame predicts that L4 is highly homologous to mammalian ribosomal protein L7a. There appear to be two genes for L4, both of which are active.

The mouse surfeit locus contains a cluster of six genes associated with four CpG-rich islands in 32 kilobases of genomic DNA

The clustered arrangement (no two adjacent genes are separated by more than 73 base pairs [bp] and two genes overlap by 133 bp at their 3' ends) of the four genes (Surf-1 to -4) identified so far in the mouse surfeit locus (T. Williams, J. Yon, C. Huxley, and M. Fried, Proc. Natl. Acad. Sci. USA 85:3527-3530, 1988) is the tightest gene clustering found in any mammalian genome to date and strongly suggests the possibility of cis-interaction and/or coregulation of gene expression. Thus, we are analyzing the surfeit genes in detail and are defining the extent of the cluster. Here we present the sequence of the entire Surf-4 gene and define the 3' and 5' extents of its mRNAs. The Surf-4 gene has heterogeneous transcriptional start sites, and its 5' end lies in a CpG-rich island. The gene specifies three mRNAs, with the two most abundant mRNAs differing in the locations of their 3' polyadenylation sites. Only the most abundant Surf-4 mRNA would overlap the 3' end of the Surf-2 gene by 133 bp. Two new genes (Surf-5 and Surf-6) have been identified in the surfeit gene cluster by Northern (RNA) blot analysis. The 5' end of Surf-6 lies within the CpG-rich island about 8 kilobases (kb) from the CpG-rich island containing the 5' end of Surf-3, and Surf-5 lies between Surf-3 and Surf-6. Thus, the cluster contains a unique arrangement of four CpG-rich islands within 32 kb associated with the 5' ends of the six surfeit genes. The neighboring CpG-rich islands have been located 500 and 100 kb distant on either side of the surfeit cluster, indicating that the end of the cluster of islands has been reached.

The mouse surfeit locus contains a cluster of six genes associated with four CpG-rich islands in 32 kilobases of genomic DNA

The clustered arrangement (no two adjacent genes are separated by more than 73 base pairs [bp] and two genes overlap by 133 bp at their 3' ends) of the four genes (Surf-1 to -4) identified so far in the mouse surfeit locus (T. Williams, J. Yon, C. Huxley, and M. Fried, Proc. Natl. Acad. Sci. USA 85:3527-3530, 1988) is the tightest gene clustering found in any mammalian genome to date and strongly suggests the possibility of cis-interaction and/or coregulation of gene expression. Thus, we are analyzing the surfeit genes in detail and are defining the extent of the cluster. Here we present the sequence of the entire Surf-4 gene and define the 3' and 5' extents of its mRNAs. The Surf-4 gene has heterogeneous transcriptional start sites, and its 5' end lies in a CpG-rich island. The gene specifies three mRNAs, with the two most abundant mRNAs differing in the locations of their 3' polyadenylation sites. Only the most abundant Surf-4 mRNA would overlap the 3' end of the Surf-2 gene by 133 bp. Two new genes (Surf-5 and Surf-6) have been identified in the surfeit gene cluster by Northern (RNA) blot analysis. The 5' end of Surf-6 lies within the CpG-rich island about 8 kilobases (kb) from the CpG-rich island containing the 5' end of Surf-3, and Surf-5 lies between Surf-3 and Surf-6. Thus, the cluster contains a unique arrangement of four CpG-rich islands within 32 kb associated with the 5' ends of the six surfeit genes. The neighboring CpG-rich islands have been located 500 and 100 kb distant on either side of the surfeit cluster, indicating that the end of the cluster of islands has been reached.

A strategy to detect and isolate an intron-containing gene in the presence of multiple processed pseudogenes

We have devised a strategy that utilizes the polymerase chain reaction (PCR) for the detection and isolation of intron-containing genes in the presence of an abundance of processed pseudogenes. The method depends on the genomic DNA sequence between the PCR primers spanning at least one intron in the gene of interest, resulting in the generation of a larger intron-containing PCR product in addition to the smaller PCR product amplified from the intronless pseudogenes. A unique intron probe isolated from the larger PCR product is used for the detection of intron-containing clones from recombinant DNA libraries that also contain pseudogene clones. This method has been used successfully for the selective isolation of an intron-containing rat L19 ribosomal protein gene in the presence of multiple pseudogenes. Analysis of a number of mammalian ribosomal protein multigene families by PCR indicates that they all contain only a single gene with introns.