The Vi element. A transposon-like repeated DNA sequence interspersed in the vitellogenin locus of Xenopus laevis

RETRACTED: A Mutant Form of MeCP2 Protein Associated with Human Rett Syndrome Cannot Be Displaced from Methylated DNA by Notch in Xenopus Embryos

MeCP2 is a DNA binding protein that represses transcription of methylated genes in vitro, but the endogenous function of MeCP2 in vivo is unclear. Here, we demonstrate that in Xenopus laevis embryos MeCP2 is a partner of the SMRT corepressor complex that regulates the expression of a neuronal repressor xHairy2a in differentiating neuroectoderm. The MeCP2/SMRT complex is bound to the promoter of the silenced xHairy2a gene and is displaced upon activation by the Notch intracellular domain (NICD). A truncated form of MeCP2 (R168X) found in patients with Rett syndrome cannot interact with the SMRT complex or fully activate xHairy2a during primary neurogenesis. This disruption of MeCP2 activity results in abnormal patterning of primary neurons during neuronal differentiation. Our results support a model whereby the dynamic association of MeCP2 with methylated DNA and the SMRT complex regulates a gene involved in cell fate decisions during primary neurogenesis in Xenopus.

The Tol2 transposable element of the medaka fish: an active DNA-based element naturally occurring in a vertebrate genome

Several DNA-based transposable elements are known to be present in vertebrate genomes, but few of them have been demonstrated to be active. The Tol2 element of the medaka fish is one such element and, therefore, is potentially useful for developing a gene tagging system and other molecular biological tools applicable to vertebrates. Towards this goal, analyses of the element at the molecular, cellular and population levels are in progress. Results so far obtained are described here.

no tail (ntl) is the zebrafish homologue of the mouse T (Brachyury) gene

The mouse T (Brachyury) gene is required for normal mesoderm development and the extension of the body axis. Recently, two mutant alleles of a zebrafish gene, no tail (ntl), have been isolated (Halpern, M. E., Ho., R. K., Walker, C. and Kimmel, C. B. (1993) Cell 75, 99–111). ntl mutant embryos resemble mouse T/T mutant embryos in that they lack a differentiated notochord and the caudal region of their bodies. We report here that this phenotype is caused by mutation of the zebrafish homologue of the T gene. While ntl embryos express mutant mRNA, they show no nuclear protein product. Later, expression of mRNA in mutants, but not in wild types, is greatly reduced along the dorsal midline where the notochord normally forms. This suggests that the protein is required for maintaining transcription of its own gene.

Genomic structure of the Xenopus laevis liver transcription factor LFB1

Liver factor B1 [LFB1, also called hepatocyte nuclear factor 1 (HNF1)] is a tissue-specific vertebrate transcription factor that is present in the liver, intestine, stomach and kidney. The LFB1 protein contains an unusual homeobox that is characterized by an insertion of 21 amino acids (aa) not found in any other homeodomain protein. We have isolated and characterized the genomic sequences encoding the LFB1 of Xenopus laevis. By comparing the genomic sequences with the cDNA clones, we could identify nine exons. In general, the position of the introns is identical to the one previously found in the rat. However, the C-terminal activation domain of LFB1 contains, in each species, an exon that is split in two in the other species. The homeobox of the X. laevis LFB1 contains an intron at exactly the position where the 21 aa typical for LFB1 are inserted. This is in agreement with the structure found in the rat gene and supports the notion that the LFB1 homeobox evolved separately from the other genes encoding homeodomain proteins.

Gene structure and alternative splicing of XFG 5-1, a X. laevis Zn finger protein with RNA homopolymer binding activity

We describe the fine-structure of the Xenopus laevis XFG 5-1 gene which codes for an RNA homopolymer binding Zn finger protein of the FAR (Finger Associated Repeat) subfamily. The gene contains six exons, i.e., a leader exon (I), four exons (II-V), each of them encoding one individual copy of the FAR repeat, and one exon (VI) encoding the linker as well as the complete multifinger-region of the corresponding protein. Isolation and characterization of distinct cDNAs revealed that primary transcripts are alternatively spliced, thereby leading either to mRNAs containing different copy numbers of the FAR repeat or, by utilization of an alternative splice acceptor site in front of exon VI, to an extension of the linker region between the FAR repeats and the multifinger domain. We also describe the fine-structure of a closely related gene, termed XFG 5-2, which is located downstream to the XFG 5-1 gene. The general structural organization in both genes is identical, but point mutations should give rise to a XFG 5-2 protein with a different number of Zn finger units.

Presence of Vi-transposon-like elements in the proopiomelanocortin gene A of Xenopus laevis does not affect gene activity

Restriction mapping of the two proopiomelanocortin (POMC) genes of the South African clawed toad Xenopus laevis revealed that POMC gene A is much larger than POMC gene B. Here we report that this size difference is mainly due to the presence of four vitellogenin (Vi)-transposon-like elements in POMC gene A, while Vi elements are absent from POMC gene B. Alignment of these elements with other Vi elements revealed a consensus sequence of 463 bp, which is bounded by a 16 bp inverted repeat and flanked by a 3 bp direct repeat. Since the amounts of mRNA produced by both POMC genes in the pars intermedia of the Xenopus pituitary are similar, the presence of the Vi-transposon-like elements in POMC gene A apparently has no effect on POMC gene expression at transcriptional or post-transcriptional levels.

Sequence analysis of the upstream regions of Xenopus laevis beta-globin genes and arrangement of repetitive elements within the globin gene clusters

The globin gene clusters of Xenopus laevis are interspersed by various different repetitive DNA elements. A specific repeat, the JH12 element, has been mapped by Southern analysis and some of its locations have been subsequently confirmed by nucleotide sequencing. JH12 family members seem to represent mobile genetic elements and display a high degree of divergence. The nucleotide sequences upstream to the adult beta I-globin gene and to the two coordinately expressed larval beta I- and beta II-globin genes have been determined and compared to those of the adult alpha-genes. Besides some repetitive DNA elements and a short sequence of rather weak homology we have found no characteristic sequence motifs to be common to the adult alpha- and beta-genes. The two larval beta-genes share one short sequence element being absent from the adult genes. This might reflect completely different sequence requirements for protein interactions and for the regulation of adult and larval globin gene expression.

Sequence organization and developmentally regulated transcription of a family of repetitive DNA sequences of Xenopus laevis

Members of a family of DNA sequences of Xenopus laevis have been cloned and sequenced. Molecular analyses revealed that these sequences are moderately repetitive and dispersed throughout the genome. The sequences of seven clones were compared. Two of the clones lie in the globin gene cluster; one 5' to the adult alpha 1 gene, and the other in the first intron of the tadpole alpha 1 gene. In all clones, the homologous region begins at the same site, but the lengths of the common regions vary from 123 bp to over 320 bp due to heterogeneous 3' ends. Some of the repeats are bracketed by direct and/or inverted repeats, and relatively large palindromes were found 5' to the common region in some clones. These characteristics, and the presence of a repeat 5' to one of a pair of duplicated alpha genes suggests that some family members may be capable of transposition. A number of interesting features were found in the sequences, including multiple elements similar to the yeast autonomously replicating sequence, and a sequence which is about 80% homologous to the first 30 bases of the SV40 enhancer. Transcription studies revealed that homologous transcripts are detectable beginning at neurulation, increase in concentration up to stage 45, and disappear by metamorphosis. Implications of these data are discussed.

Precursor-product relationship between vitellogenin and the yolk proteins as derived from the complete sequence of a Xenopus vitellogenin gene

In Xenopus laevis four estrogen-responsive genes are expressed simultaneously to produce vitellogenin, the precursor of the yolk proteins. One of these four genes, the gene A2, was sequenced completely, as well as cDNAs representing 75% of the coding region of the gene. From this data the exon-intron structure of the gene was established, revealing 35 exons that give a transcript of 5,619 bp without the poly A-tail. This A2 transcript encodes a vitellogenin of 1,807 amino acids, whose structure is discussed with respect to its function. At the nucleic acid as well as at the protein level no extensive homologies with any sequences other than vitellogenin were observed. Comparison of the amino acid sequence of the vitellogenin A2 molecule with biochemical data obtained from the different yolk proteins allowed us to localize the cleavage products on the vitellogenin precursor as follows: NH2 - lipovitellin I - phosvitin (or phosvette II - phosvette I) - lipovitellin II - COOH.

The distribution of the dinucleotide CpG and cytosine methylation in the vitellogenin gene family

Sequence data from regions of five vertebrate vitellogenin genes were used to examine the frequency, distribution, and mutability of the dinucleotide CpG, the preferred modification site for eukaryotic DNA methyltransferases. The observed level of the CpG dinucleotide in all five genes was markedly lower than that expected from the known mononucleotide frequencies. CpG suppression was greater in introns than in exons. CpG-containing codons were found to be avoided in the vitellogenin genes, but not completely despite the redundancy of the genetic code. Frequency and distribution patterns of this dinucleotide varied dramatically among these otherwise closely related genes. Dense clusters of CpG dinucleotides tended to appear in regions of either functional or structural interest (e.g., in the transposon-like Vi-element of Xenopus) and these clusters contained 5-methylcytosine (5 mC). 5 mC is known to undergo deamination to form thymidine, but the extent to which this transition occurs in the heavily methylated genomes of vertebrates and its contribution to CpG suppression are still unclear. Sequence comparison of the methylated vitellogenin gene regions identified C----T and G----A substitutions that were found to occur at relatively high frequencies. The predicted products of CpG deamination, TpG and CpA, were elevated. These findings are consistent with the view that CpG distribution and methylation are interdependent and that deamination of 5 mC plays an important role in promoting evolutionary change at the nucleotide sequence level.

Linkage arrangement in the vitellogenin gene family of Xenopus laevis as revealed by gene segregation analysis

Using restriction fragment length polymorphism (RFLP) we have analyzed the segregation of alleles of the different vitellogenin genes of Xenopus laevis. The results demonstrate that the four genes whose expression is controlled by oestrogen, form two linkage groups. The genes A1, A2 and B1 are linked genetically whereas the fourth gene, the gene B2, segregates independently. The possible origin of this unexpected arrangement is discussed.

Conserved sequence motifs upstream from the co-ordinately expressed vitellogenin and apoVLDLII genes of chicken

The vitellogenin and apoVLDLII yolk protein genes of chicken are transcribed in the liver upon estrogenization. To get information on putative regulatory elements, we compared more than 2 kb of their 5' flanking DNA sequences. Common sequence motifs were found in regions exhibiting estrogen-induced changes in chromatin structure. Stretches of alternating pyrimidines and purines of about 30-nucleotides long are present at roughly similar positions. A distinct box of sequence homology in the chicken genes also appears to be present at a similar position in front of the vitellogenin genes of Xenopus laevis, but is absent from the estrogen-responsive egg-white protein genes expressed in the oviduct. In front of the vitellogenin (position -595) and the VLDLII gene (position -548), a DNA element of about 300 base-pairs was found, which possesses structural characteristics of a mobile genetic element and bears homology to the transposon-like Vi element of Xenopus laevis.