The MT family of mouse DNA is made of short interspersed repeated elements

Mouse retrotransposons: sequence structure, evolutionary age, genomic distribution and function

Retrotransposons are transposable elements that are transposed via transcription and reverse transcription. Their copies have accumulated in the genome of mammals, occupying approximately 40% of mammalian genomic mass. These copies are often involved in numerous phenomena, such as chromatin spatial organization, gene expression, development and disease, and have been recognized as a driving force in evolution. Different organisms have gained specific retrotransposon subfamilies and retrotransposed copies, such as hundreds of Mus-specific subfamilies with diverse sequences and genomic locations. Despite this complexity, basic information is still necessary for present-day genomic and epigenomic studies. Herein, we describe the characteristics of each subfamily of Mus-specific retrotransposons in terms of sequence structure, phylogenetic relationships, evolutionary age, and preference for A or B compartments of chromatin.

Stage-specific expression of two neighboring Crlz1 and IgJ genes during B cell development is regulated by their chromatin accessibility and histone acetylation

The IgJ gene is expressed in the plasma cell stage. However, its neighboring charged amino acid-rich leucine zipper 1 (Crlz1) gene, which is mapped 30 kb upstream of the IgJ gene in mice, is shown to be expressed in the pre-B cell stage. These stage-specific expressions of two neighboring genes are found to be regulated by their chromatin accessibility and acetylation. Hypersensitive site 1 on the IgJ promoter is opened in the plasma cells, whereas hypersensitive sites 9/10 on the Crlz1 promoter are opened in the pre-B cells. Furthermore, H3 and H4 histones toward the chromatin of the Crlz1 gene are found to be hyperacetylated, especially on H3, in the pre-B cells, whereas those toward the chromatin of the IgJ gene are found to be hyperacetylated in the plasma cells. Consistently, the hyperacetylation of H3 and H4 toward the chromatin of the IgJ gene but not the Crlz1 gene is induced by an IL-2 treatment of BCL1, which is a model cell line for studying the terminal differentiation of B cells.

Identification, structural characterization, and tissue distribution of Tsg-5: a new TNF-stimulated gene

Using DDRT-PCR, we compared the mRNA content of untreated and TNF-treated mouse embryonic fibroblasts (MEFs). Among differentially represented fragments, we identified and cloned a novel TNF-stimulated gene named Tsg-5. This gene, mapped to mouse chromosome 14, has three exons that can be alternatively spliced giving rise to two mRNA species, one spanning three exons and another that skips the second exon. Analysis of full-length Tsg-5 cDNA revealed a potential start codon within exon 2 encoding an ORF of 40 amino-acids. No homology with known mouse or human sequences, neither at the nucleotide nor at the amino-acid level could be found in public databases. In MEFs, Tsg-5 is induced by tumor necrosis factor-alpha (TNF) and IL-1 beta, albeit with distinct kinetics. TNF-induced Tsg-5 expression is NF-kappa B-dependent as it was inhibited by MG132, lactacystin, Bay 11-7083, and Bay 11-7085. Analysis of Tsg-5 expression in vivo revealed that the gene and its encoded polypeptide are constitutively expressed in the thymus and ovary, whereas, in LPS-treated mice, Tsg-5 mRNA can be detected in the spleen, lung, and brain. Our data suggest that Tsg-5 encodes a new, rare transcript, with a very tight regulation of expression and differential splicing.

Chromosomal location of murine disabled-2 gene and structural comparison with its human ortholog

Disabled-2 (Dab2) is one of the two mammalian orthologs of the Drosophila Disabled. The three spliced forms, p96, p93, and p67 of murine Dab2 cDNAs were first isolated as phosphoproteins functioning in the macrophage CSF-1 signal transduction pathway. Subsequently, the involvement of Dab2 in ovarian cancer development has been investigated: Dab2 expression is lost or greatly diminished in breast and ovarian cancers, and gene deletions have been found. Regulation of Disabled-2 expression is also found to be important in development and physiological functions. Structural information of the murine Dab2 gene is essential for studies of transcription regulation and gene function in mouse models. In this study, the mouse Dab2 gene coding sequence was identified and sequenced from three lambda phage clones containing the gene. Two BAC clones of mouse genomic DNA were also used to identify the sequences of the non-coding first exon and promoter. The first exon is separated from the second exon by a large (15 kb) intron. The mouse gene is about 40 kb in size and consists of 15 exons, producing a 3.6 kb message. The translation initiation site resides in the middle of the second exon. The mouse Dab2 gene structure is very similar to that of its human ortholog in exon/intron sizes and promoter sequences. The chromosomal localization of mouse Dab2 was mapped by FISH to chromosome 15A2, a site of syntax with the human 5p12 where human Dab2 gene resides. The information on the mouse Dab2 gene structure and promoter will be invaluable in studies of the involvement of Dab2 gene in cancer, expression, physiological function, and development in mouse models.

Functional interactions between an atypical NF-kappaB site from the rat CYP2B1 promoter and the transcriptional repressor RBP-Jkappa/CBF1

The phenobarbital-inducible rat cytochrome P450 (CYP) 2B1 and 2B2 proteins are encoded by homologous genes whose promoters contain a mammalian-apparent long terminal repeat retrotransposon (MaLR). An NF-kappaB-like site within the MaLR forms multiple protein-DNA complexes with rat liver and HeLa cell nuclear extracts. Using antibody supershift assays, we have identified these complexes as NF-kappaB and RPB-Jkappa/CBF1. Competition assays using a series of single site mutant oligonucleotides reveal that the recognition sites for these two factors overlap. We also show that the CYP2B1/2 NF-kappaB element, but not the Igkappa NF-kappaB element, can repress transcription in vitro when positioned upstream of the heterologous adenovirus major late core promoter. In addition, RBP-Jkappa over-expressed in COS-7 cells repressed expression in vivo from an SV40-luciferase reporter construct that contained the CYP2B1/2 NF-kappaB element. Finally, we observe similar levels of NF-kappaB and RBP-Jkappa binding activities in nuclear extracts prepared from control and phenobarbital-induced rat livers. The results suggest that RBP-Jkappa/CBF1 binds an atypical NF-kappaB site in the CYP2B1/2 promoters and may help to maintain a low level of expression in the absence of inducer.

Genomic structure of murine Rab11 family members

Rab11a, Rab11b, and Rab25 in mammals are thought to comprise a subfamily of Rab proteins, although Rab25 has two amino acid differences in its effector domain. We have isolated and characterized the genomic sequences of murine Rab11a and Rab25 and compared them with those of previously characterized mammalian Rab genes. The Rab11a gene spans 29 kb and Rab25 spans 9 kb. The genes have TATA-less promoters, but contain GC-rich areas in their upstream 5' regions. Both genes have 5 exons, with the introns containing characteristic repeats. Rab11a has an unusually long 8. 5-kb fourth intron. The Rab11a and Rab25 genes are localized to chromosomes 9C and 3E3/F1, respectively. The overall organization of the Rab11a, Rab11b, and Rab25 genes is similar, with homologous exon-intron boundaries, and differs markedly from those of Rab3A and Rab1A. These results confirm that Rab11A, Rab11b, and Rab25 represent a closely related gene family.

The gene structure and promoter analysis of mouse lymphocyte signal transduction molecule alpha 4 that is related to the yeast TAP42 involved in a rapamycin-sensitive pathway

The mouse alpha 4 phosphoprotein encoding a component associated with the B cell antigen receptor (BCR)-mediated signal transduction is suggested to be involved in a unique rapamycin-sensitive pathway. We studied the structure and the molecular mechanism of the expression of alpha 4 gene by isolating two phage clones, named #10 and #23, covering entire exons of the mouse alpha 4 gene. The alpha 4 gene is located within about 25 kb and composed of six exons. To analyze the regulation of alpha 4 gene expression, we determined the nucleotide sequence toward 2 kb upstream of the translation start site of the alpha 4 gene. The 5'-flanking region does not contain a typical TATA box or the initiation consensus sequence, but it contains a CCAAT box, E-boxes, and several DNA binding motifs such as c-Myc, c-Myb, and c-Ets. Transcription of the alpha 4 gene starts at four different sites, determined by primer extension analysis, that were surrounded by Y-rich sequences. We further characterized the functional promoter of the alpha 4 gene at the region between -263 and the transcription start site of alpha 4 gene by luciferase assay system and suggested that the 5' upstream region of alpha 4 gene contains the silencer element of MT repetitive sequence.

Isolation, characterization and in vivo analysis of the murine calbindin-D28K upstream regulatory region

The genomic locus containing the murine calbindin-D28K gene has been isolated and partially characterized. Genomic cloning revealed an exon/intron chromosomal structure very similar to the avian gene previously described. The ability of the calbindin-D28K upstream region to direct cell-specific expression was tested in vivo. Varying lengths of upstream sequence were used to drive expression of lacZ in transgenic mice. Characterization of 23 transgenic mouse lines revealed that even as much as 3.0 kb of upstream sequence was unable to direct expression independently of integration site effects, suggesting the absence of important elements. Despite the small number of expressing transgenic lines and the great variability, there was a tendency of cell specificity of transgene expression exhibited in distinct brain regions. In the cerebellum, Purkinje cell-specific expression was observed with the shortest (1.0 kb) upstream sequence tested. Specificity of transgene expression in Purkinje cells was abolished with longer portions of upstream sequence. The same observation was made for transgene expression in granule cells of the dentate gyrus, while the opposite effect was observed for expression in CA1 hippocampal cells. The absence of any transgenic lines exhibiting appropriate transgene expression in the kidney suggested that the VDREs described previously for the murine calbindin gene are not sufficient to direct kidney expression in vivo. It is concluded that 3.0 kb of calbindin upstream sequence includes the regulatory elements dictating a portion of cell-specificity in the CNS of transgenic mice, albeit lacking regions that allow expression independently of chromosomal effects.

Recruitment of multiple alleles within the Eb recombinational hotspot in murine MHC

Genetic recombination has been proposed to have played a major role in generating the extensive polymorphism that distinguishes the genes of the major histocompatibility complex (MHC). The proximal region of the murine H-2 represents a unique segment of DNA encompassing at least four hotspots for meiotic recombination. One of these hotspots lies within the second intron of the class II Eb gene and has been defined at the nucleotide level for a number of simple two-allele crosses. In this report we studied two crosses in which one or both parents in themselves were H2Eb recombinants and three alleles were present within the hotspots of each pair of the parental haplotypes. Nucleotide analysis indicated that the break points in these secondary recombinants, like those in the primary recombinants, were also discrete and clustered within the H2Eb second intron. Thus, in one instance two and in the other instance three alleles were present within the hotspots of these recombinants. These observations strongly suggest that meiotic recombination could be an important mechanism contributing to MHC polymorphism.

Identification of a new, abundant superfamily of mammalian LTR-transposons

A new superfamily of mammalian transposable genetic elements is described with an estimated 40,000 to 100,000 members in both primate and rodent genomes. Sequences known before as MT, ORR-1, MstII, MER15 and MER18 are shown to represent (part of) the long terminal repeats of retrotransposon-like elements related to THE1 in humans. These transposons have structural similarities to retroviruses. However, the putative product of a 1350 base pair open reading frame detected in the consensus internal sequence of THE1 does not resemble retroviral proteins. The elements are named 'Mammalian apparent LTR-retrotransposons' (MaLRs). The internal sequence is usually found to be excised. Their presence in rodents, artiodactyls, lagomorphs, and primates, the divergence of the individual elements from their consensus, and the existence of a probably orthologous element in mouse and man suggest that the first MaLRs were distributed before the radiation of eutherian mammals 80-100 million years ago. MaLRs may prove to be very helpful in determining the evolutionary branching pattern of mammalian orders and suborders.

Sequence variations and promoter activities of long terminal repeats from rat intracisternal A-particles

Nucleotide sequences of three novel rat long terminal repeats (LTR) of intracisternal A-particles (IAP) were determined and compared with two previously published solitary rat IAP LTRs from the genomic clone H12 (Furter et al. (1989) J. Biol. Chem. 264, 18276-18279) and from the upstream region of the oncomodulin (OM) gene (Banville and Boie (1989) J. Mol. Biol. 207, 481-490). These five LTRs have a length of 286 to 370 bp and show the major variability within the U3 region. The CCAAT and the TATA boxes, the AATAAA polyadenylation signals and the CA polyadenylation sites are well conserved in sequence and position in all five LTRs, whereas several putative transcriptional factor binding sites in the U3 domain show considerable heterogeneity. The transcriptional activities of three LTRs were tested in transient gene expression assays using the human growth hormone (hGH) reporter gene in chemically transformed T14c cells which produce considerable amounts of oncomodulin. Promoter strengths of the three investigated LTRs varied considerably.

Spontaneous mutation at the hypervariable mouse minisatellite locus Ms6-hm: flanking DNA sequence and analysis of germline and early somatic mutation events

Hypervariability at minisatellite loci is maintained by spontaneous mutation to new-length alleles. At the most variable loci, mutation rate is directly measurable by pedigree analysis. The mouse minisatellite locus Ms6-hm has a germline mutation rate of 2.5% per gamete and is therefore one of the most unstable loci yet identified in the mouse genome. Mutation events at this locus also occur during early mouse development, resulting in mice mosaic for cells carrying a common non-parental allele in different somatic tissues and the germline. The DNA sequence flanking Ms6-hm is rich in dispersed repetitive elements; the minisatellite array has expanded from within a member of the Mouse Transcript family which is flanked by two additional Mouse Transcript elements, and a B2 element lies further 3' to the minisatellite. To define the characteristics of mutation events at Ms6-hm we have analysed 19 germline and 13 somatic length-change events. Germline mutation events at Ms6-hm are not accompanied by the exchange of flanking markers in three informative mutant alleles analysed.

Characterization of a highly unstable mouse minisatellite locus: evidence for somatic mutation during early development

A highly unstable mouse minisatellite locus, Ms6-hm, has been identified in mouse DNA fingerprints produced by cross-hybridization with human minisatellite probe 33.6. A 7-kb allele of Ms6-hm was cloned from a C57BL/6J mouse and collapsed to a 400-bp plasmid insert on propagation in Escherichia coli due to loss of the majority of minisatellite repeat units. Sequence analysis revealed that Ms6-hm has evolved by amplification within a member of the MT (mouse transcript) family of interspersed repetitive elements. Linkage analysis localized Ms6-hm near the brown coat color gene (b) on chromosome 4. Multiallelism and heterozygosity at this locus within inbred strains result from a high germline mutation rate to new-length alleles (2.5% per gamete). Mice mosaic for cells carrying a nonparental allele in somatic tissue, and in some cases also in the germline, provide evidence for additional, somatic, mutation events at Ms6-hm. In two mosaic mice the fraction of cells containing the nonparental allele has been shown to be indistinguishable in different adult tissues. These somatic mutation events at Ms6-hm must therefore occur very early in development, preceding the allocation of somatic lineages, and the same pool of primitive ectoderm cells must contribute equally to all somatic tissues. Under low-stringency hybridization conditions the collapsed subclone of Ms6-hm cross-hybridizes to other unstable loci in the mouse genome to generate a novel and highly individual specific mouse DNA fingerprint.

Major rearrangement of cellular DNA in the vicinity of integrated polyomavirus DNA

The Cyp cell line was produced by transforming mouse embryo cells at the restrictive temperature with an early thermosensitive mutant of polyomavirus (Py). Transfer of Cyp cells to the nonrestrictive temperature causes excision to occur at a single chromosomal site carrying viral DNA, and leads to the production of infectious virus. We have attempted to elucidate the recombination event that occurred during the integration of Py DNA in this inducible line. Physical characterization of two recombinant DNAs-one selected from a genomic library of normal mouse DNA and the other constructed from the unoccupied allele of the Cyp integration site-indicates that generation of the Cyp line has involved the joining of not only viral DNA to a cellular alpha site, but also the cellular alpha site to a cellular alpha site to cellular beta site. Hence, previously described hybrid excision products from the Cyp line were made of mouse DNA segments representing two distinct cellular sites. The alpha-beta joining may play a role in the expression of integrated Py DNA.