A Drosophila gene containing the opa repetitive element is exclusively expressed in adult male abdomens

E and ID proteins regulate cell chirality and left-right asymmetric development in Drosophila

How left-right (LR) asymmetric forms in the animal body is a fundamental problem in Developmental Biology. Although the mechanisms for LR asymmetry are well studied in some species, they are still poorly understood in invertebrates. We previously showed that the intrinsic LR asymmetry of cells (designated as cell chirality) drives LR asymmetric development in the Drosophila embryonic hindgut, although the machinery of the cell chirality formation remains elusive. Here, we found that the Drosophila homologue of the Id gene, extra macrochaetae (emc), is required for the normal LR asymmetric morphogenesis of this organ. Id proteins, including Emc, are known to interact with and inhibit E-box-binding proteins (E proteins), such as Drosophila Daughterless (Da). We found that the suppression of da by wild-type emc was essential for cell chirality formation and for normal LR asymmetric development of the embryonic hindgut. Myosin ID (MyoID), which encodes the Drosophila Myosin ID protein, is known to regulate cell chirality. We further showed that Emc-Da regulates cell chirality formation, in which Emc functions upstream of or parallel to MyoID. Abnormal Id-E protein regulation is involved in various human diseases. Our results suggest that defects in cell shape may contribute to the pathogenesis of such diseases.

Association studies of the HOPA dodecamer duplication variant in different subtypes of autism

The HOPA gene in Xq13 is coding for a protein involved in a nuclear thyroid receptor complex. Previous studies suggested association of the dodecamer duplication in the OPA-repeat region in exon 43 (according to the genomic database sequence) with autism, mental retardation, and schizophrenia/hypothyroidism. We determined the frequency of this 12 bp duplication variant in a sample of 155 patients divided in different subtypes of autism, 278 parents of those patients, and 157 control individuals. The allele frequency of the duplication variant was not significantly different between autistic patients, their parents, and the control group. Therefore, it is unlikely that this 12 bp duplication variant of the HOPA gene has major relevance to the susceptibility to different subtypes of autism at least in this German patient sample. In addition, we identified a third variant with a 15 bp deletion in the OPA-repeat region, recently described by another group, in one autistic patient. This third allele was also present in the patient's nonautistic mother and sister, who are heterozygous for this variant, but could not be detected in any other individual genotyped in this study. Expression analysis revealed transcription of all three allelic variants in lymphoblastoid cell lines. Furthermore, we identified a new splice variant that utilizes an additional 9 bp of the 3' intron subsequent to exon 39. Both alternative transcripts are coexpressed in all fetal and adult tissues examined.

Expression analysis of an Arabidopsis C2H2 zinc finger protein gene

C2H2 zinc finger protein genes encode nucleic acid-binding proteins involved in the regulation of gene activity. AtZFP1 (Arabidopsis thaliana zinc finger protein 1) is one member of a small family of C2H2 zinc finger-encoding sequences previously characterized from Arabidopsis. The genomic sequence corresponding to the AtZFP1 cDNA has been determined. Molecular analysis demonstrates that AtZFP1 is a unique, intronless gene which encodes a 1100 nucleotides mRNA highly expressed in roots and stems. A construct in which 2.5 kb of AtZFP1 upstream sequences is linked to the beta-glucuronidase gene was introduced into Arabidopsis by Agrobacterium-mediated transformation of roots. Histochemical analysis of transgenic Arabidopsis carrying the AtZFP1 promoter: beta-glucuronidase fusion shows good correlation with RNA blot hybridization analysis. This transgenic line will be a useful tool for analyzing the regulation of AtZFP1 to further our understanding of its function.

Characterization of a family of Arabidopsis zinc finger protein cDNAs

Work from animal systems indicates that C2H2 zinc finger proteins play an important role in development, and this is likely true for plant systems as well. To address this question we have used the sequence information from a previously isolated Arabidopsis thaliana C2H2 zinc finger protein gene to isolate additional cDNAs belonging to this gene family. While zinc finger genes isolated from other organisms encode multiple copies of this domain, the eight cDNAs isolated from Arabidopsis each contain only a single zinc finger. Outside of the finger region there is little sequence identity or similarity, although features characteristic of transcription factors are evident. While these genes are related, hybridization analysis indicates that each of them is a unique gene in the Arabidopsis genome. Analysis of mRNA demonstrates that the genes are expressed in different but overlapping sets of organs in the plant. These results are discussed in the light of recent analysis of zinc finger genes from other plant systems.

The SRP9/14 subunit of the signal recognition particle (SRP) is present in more than 20-fold excess over SRP in primate cells and exists primarily free but also in complex with small cytoplasmic Alu RNAs

The heterodimeric protein SRP9/14 bound to the Alu sequences of SRP RNA is essential for the translational control function of the signal recognition particle (SRP). The Alu RNAs of primate cells are believed to be derived from SRP RNA and have been shown to bind to an SRP14-related protein in vitro. We have used antibodies to characterize SRP9/14 and examine its association with small RNAs in vivo. Although SRP9 proteins are the same size in both rodent and primate cells, SRP14 subunits are generally larger in primate cells. An additional alanine-rich domain at the C-terminus accounts for the larger size of one human isoform. Although the other four SRP proteins are largely assembled into SRP in both rodent and primate cells, we found that the heterodimer SRP9/14 is present in 20-fold excess over SRP in primate cells. An increased synthesis rate of both proteins may contribute to their accumulation. The majority of the excess SRP9/14 is cytoplasmic and does not appear to be bound to any small RNAs; however, a significant fraction of a small cytoplasmic Alu RNA is complexed with SRP9/14 in a 8.5 S particle. Our findings that there is a large excess of SRP9/14 in primate cells and that Alu RNAs are bound to SRP9/14 in vivo suggest that this heterodimeric protein may play additional roles in the translational control of gene expression and/or Alu transcript metabolism.

Genomic organization of the human catechol O-methyltransferase gene and its expression from two distinct promoters

Human genomic DNA fragments containing catechol O-methyltransferase (COMT) sequences were isolated and the exon-intron structure analysed by sequencing, PCR and comparing to the human COMT cDNA sequences. The gene contains six exons, of which exons 1 and 2 are noncoding. MB-ATG and S-ATG codons, responsible for the initiation of translation of the membrane-bound (MB) and soluble (S) forms of the enzyme, are located in exon 3. Two distinct COMT-specific transcripts, 1.3 kb and 1.5 kb, were detected in various human tissues and cell lines. Different quantities of the shorter COMT-specific mRNA in the tissues studied suggest a tissue-specific regulation of the COMT gene at transcriptional level. Mapping of the 5' ends of the COMT mRNAs showed that transcription initiates at multiple sites in two separate DNA regions, which are preceded by functional promoter sequences. The proximal promoter (P1), located between the two translation initiation codons and extending approximately 200 bp upstream of the MB-ATG initiation codon, apparently gives rise to the 1.3-kb S-COMT mRNA (S-mRNA). The distal promoter (P2) is located in a DNA fragment in front of and partly overlapping the transcription-start region of the 1.5-kb transcript, suggesting that it controls the expression of this MB-mRNA. Similarities between the rat and human COMT gene promoters are analyzed.

The novel Notch homologue mouse Notch 3 lacks specific epidermal growth factor-repeats and is expressed in proliferating neuroepithelium

In Drosophila, the Notch gene is pivotal for cell fate decisions at many stages of development and, in particular, during the formation of the nervous system. Absence of Notch results in the generation of excessive numbers of neural cells at the expense of epidermal cells. Two previously identified mammalian Notch homologous encode all the principal features of the Drosophila gene, e.g. 36 EGF-repeats and 3 Notch/lin-12 repeats extracellularly and 6 intracellular cdc10/SWI6 repeats. We report here the characterisation of a third mammalian homologue, mouse Notch 3, which shares the same remarkable conservation relative to the Drosophila gene as the two previously identified homologues, but with three important distinctions. First, Notch 3 specifically lacks the equivalent of EGF-repeat 21; second, it lacks an EGF-repeat-sized region comprising parts of EGF-repeats 2 and 3; and third, it encodes a considerably shorter intracellular domain. The Notch 3 gene is expressed at high levels in proliferating neuroepithelium and expression is downregulated at later stages. The expression patterns of the Notch 1, 2 and 3 genes are quite distinct during central nervous system (CNS) development, and all possible combinations of expression, i.e. none, one, two, or all three genes, are seen, suggesting a combinatorial code of Notch function in mammals. Considering the predominantly early expression in CNS and its distinct structural features, the Notch 3 gene is likely to contribute significantly to vertebrate Notch function during CNS development.

A cDNA encoding an ADP/ATP carrier from the mosquito Anopheles gambiae

Two cDNAs are described from Anopheles gambiae that correspond to the ADP/ATP carrier or translocase. The clones are identical except for minor differences in the 5' non-coding region and in the lengths of the poly-A tails. They code for mRNAs of 1261 and 1263 bp and contain one open reading frame of 906 bp. A probe made from the 1263 bp cDNA hybridized to bands of approximately 1260 and 1700 bp on developmental Northern blots. The putative 300 amino acid peptide sequence shows from 53.4-78.5% identity to AAC peptide sequences from a range of organisms from Zea mays to human. Both clones mapped to region 26a on the left arm of chromosome 2 in An. gambiae.

Opa-like repeats in the genome of the Medfly Ceratitis capitata

The sequence determination of several genomic clones isolated from the Mediterranean fruitfly Ceratitis capitata identified the existence of opa-like repeats, often more than one being clustered in small chromosomal segments. These repeats have previously been shown to consist of stretches of tandemly reiterated glutamine-encoding residues, and they are found in multiple genes of several organisms. Most of the repeats described here are flanked or interrupted by stop codons in all reading frames and, thus, could not possibly be part of protein-coding sequences. Furthermore, these repeats, of which there are several hundred in the genome of the Medfly, can be used effectively for the determination of sequence polymorphisms, providing a convenient approach to obtain additional landmarks for the construction of genomic maps of this economically important insect.

Distinct families of site-specific retrotransposons occupy identical positions in the rRNA genes of Anopheles gambiae

Two distinct site-specific retrotransposon families, named RT1 and RT2, from the sibling mosquito species Anopheles gambiae and A. arabiensis, respectively, were previously identified. Both were shown to occupy identical nucleotide positions in the 28S rRNA gene and to be flanked by identical 17-bp target site duplications. Full-length representatives of each have been isolated from a single species, A. gambiae, and the nucleotide sequences have been analyzed. Beyond insertion specificity, RT1 and RT2 share several structural and sequence features which show them to be members of the LINE-like, or non-long-terminal-repeat retrotransposon, class of reverse transcriptase-encoding mobile elements. These features include two long overlapping open reading frames (ORFs), poly(A) tails, the absence of long terminal repeats, and heterogeneous 5' truncation of most copies. The first ORF of both elements, particularly ORF1 of RT1, is glutamine rich and contains long tracts of polyglutamine reminiscent of the opa repeat. Near the carboxy ends, three cysteine-histidine motifs occur in ORF1 and one occurs in ORF2. In addition, each ORF2 contains a region of sequence similarity to reverse transcriptases and integrases. Alignments of the protein sequences from RT1 and RT2 reveal 36% identity over the length of ORF1 and 60% identity over the length of ORF2, but the elements cannot be aligned in the 5' and 3' noncoding regions. Unlike that of RT2, the 5' noncoding region of RT1 contains 3.5 copies of a 500-bp subrepeat, followed by a poly(T) tract and two imperfect 55-bp subrepeats, the second spanning the beginning of ORF1. The pattern of distribution of these elements among five siblings species in the A. gambiae complex is nonuniform. RT1 is present in laboratory and wild A. gambiae, A. arabiensis, and A. melas but has not been detected in A. quadriannulatus or A. merus. RT2 has been detected in all available members of the A. gambiae complex except A. merus. Copy number fluctuates, even among the offspring of individual wild female A. gambiae mosquitoes. These findings reflect a complex evolutionary history balancing gain and loss of copies against the coexistence of two elements competing for a conserved target site in the same species for perhaps millions of years.

Distinct families of site-specific retrotransposons occupy identical positions in the rRNA genes of Anopheles gambiae

Two distinct site-specific retrotransposon families, named RT1 and RT2, from the sibling mosquito species Anopheles gambiae and A. arabiensis, respectively, were previously identified. Both were shown to occupy identical nucleotide positions in the 28S rRNA gene and to be flanked by identical 17-bp target site duplications. Full-length representatives of each have been isolated from a single species, A. gambiae, and the nucleotide sequences have been analyzed. Beyond insertion specificity, RT1 and RT2 share several structural and sequence features which show them to be members of the LINE-like, or non-long-terminal-repeat retrotransposon, class of reverse transcriptase-encoding mobile elements. These features include two long overlapping open reading frames (ORFs), poly(A) tails, the absence of long terminal repeats, and heterogeneous 5' truncation of most copies. The first ORF of both elements, particularly ORF1 of RT1, is glutamine rich and contains long tracts of polyglutamine reminiscent of the opa repeat. Near the carboxy ends, three cysteine-histidine motifs occur in ORF1 and one occurs in ORF2. In addition, each ORF2 contains a region of sequence similarity to reverse transcriptases and integrases. Alignments of the protein sequences from RT1 and RT2 reveal 36% identity over the length of ORF1 and 60% identity over the length of ORF2, but the elements cannot be aligned in the 5' and 3' noncoding regions. Unlike that of RT2, the 5' noncoding region of RT1 contains 3.5 copies of a 500-bp subrepeat, followed by a poly(T) tract and two imperfect 55-bp subrepeats, the second spanning the beginning of ORF1. The pattern of distribution of these elements among five siblings species in the A. gambiae complex is nonuniform. RT1 is present in laboratory and wild A. gambiae, A. arabiensis, and A. melas but has not been detected in A. quadriannulatus or A. merus. RT2 has been detected in all available members of the A. gambiae complex except A. merus. Copy number fluctuates, even among the offspring of individual wild female A. gambiae mosquitoes. These findings reflect a complex evolutionary history balancing gain and loss of copies against the coexistence of two elements competing for a conserved target site in the same species for perhaps millions of years.