Redesigning the body plan of Drosophila by ectopic expression of the homoeotic gene Antennapedia

Genetic and molecular studies on the expression of Antennapedia (Antp) have suggested that this gene specifies mainly the second thoracic segment. On the basis of our molecular analysis of dominant gain-of-function mutants we have postulated that the transformation of antennae into second legs is due to the ectopic overexpression of the Antp+ protein. This hypothesis was tested by inserting the complementary DNA encoding the normal Antp protein into a heat-shock expression vector and subsequent germ-line transformation. As predicted, heat induction at defined larval stages leads to the transformation of antennae into second legs. The dorsal part of the head can also be transformed into second thoracic structures (scutum) indicating that Antp indeed specifies the second thoracic segment. By ectopic overexpression of the Antp protein the body plan of the fruit fly can be altered in a predictable way.     

The correct activation of Antennapedia and bithorax complex genes requires the fushi tarazu gene

In the Drosophila embryo the establishment and specification of metameric units depends upon the selective activation of the segmentation and the homoeotic selector genes. The former are necessary for establishing the appropriate number of metameric or parasegmental units, whereas the latter control the pathways of differentiation followed by particular parasegments. Classical embryological manipulations have show n that these processes must be closely coordinated during normal development. However, previous studies of pair-rule genes have led to the suggestion that the specification of segmental identity proceeds independently of the establishment of metameres as physical units. These apparently conflicting perspectives can be reconciled by envisaging a common maternally derived positional information system which is independently interpreted by the components of both processes. In the case of the partitioning process, the gap and pair-rule genes would be instrumental in translating this information, whereas the activation of the homeotic genes would be mediated via other intermediaries (see ref. 9 for review). It is difficult to see, however, how such a system could ensure the precise regulation of the tw o types of genes implicit in the final differentiated pattern. This difficulty has led to the suggestion that the segmentation mechanism must define the precise boundaries of selector gene expression. Here we confirm this suggestion and propose that the gene fushi tarazu plays a key role in this process, integrating the processes of metameric partitioning and regional specification in the Drosophila embryo.     

In vivo binding pattern of a trans-regulator of homoeotic genes in Drosophila melanogaster

The specification and maintenance of the metameric pattern in Drosophila melanogaster is regulated by complicated gene interactions. The differential expression of the homoeotic genes of the Antennapedia complex (ANT-C) and bithorax complex (BX-C), which determine segmental identities, is partly controlled by cross-regulatory interactions of loci within the two clusters and partly by trans-acting factors located outside the two complexes. One of the trans-regulatory genes, Polycomb (Pc), acts as a repressor of the ANT-C and BX-C. Mutations of Polycomb result in a complete depression of the homoeotic genes, leading to abdominal transformations of all body segments. Polycomb is part of a large class of trans-regulatory genes (Pc-group), estimated to comprise up to 40 loci. We have raised antibodies against the Polycomb protein, and, using an improved immunostaining technique, showed that the Polycomb protein binds to 60 discrete sites along the polytene chromosomes of salivary glands. These sites comprise the ANT-C and the BX-C as well as several locations of Pc-group genes. This is the first clear evidence for a direct interaction of Polycomb with homoeotic loci and other Pc-group genes.     

A conserved sequence at c-myc oncogene chromosomal translocation breakpoints in plasmacytomas

Many recent studies have shown that chromosomal translocation breakpoints frequently occur near cellular proto-oncogenes (reviewed in ref. 1). In both mouse plasmacytomas and Burkitt lymphomas, the c-myc oncogene becomes joined to an immunoglobulin heavy-chain gene in a head-to-head configuration. Within c-myc, the breaks frequently occur near the first exon-intron boundary, while within the immunoglobulin gene the breaks usually involve sequences directing heavy-chain switching. It has been assumed that the translocations represent abortive immunoglobulin switching events which have activated the c-myc gene for a role in tumour formation. However, sequence analysis of the c-myc gene does not reveal any apparent similarity to the immunoglobulin switch signals. With these results in mind, we have determined the precise breakpoints within c-myc for two plasmacytoma lines in order to search for any common features that may shed some light on the mechanism of chromosomal translocation. We report here that the tetranucleotide sequence GAGG occurs close to the breakpoint in five out of six translocations, and so may be a sequence recognized by either the enzymes that catalyse immunoglobulin heavy-chain switching, or some other DNA-cleaving activity.     

DNA序列的一种分类方法

基于小波变换和相关技术,提出了一种DNA序列的分类方法.首先将DNA序列转换成数字序列,然后对此序列进行Matlab快速分解,计算未知类别序列与已知类别序列的相关系数,由此判定序列的类别.结果表明,该方法是切实可行的.     

A conserved sequence in the immunoglobulin J kappa-C kappa intron: possible enhancer element

Several functionally important genetic elements (such as the TATA box, mRNA splice sequences, poly(A) addition signal) were first detected as short segments of unexplained sequence homology within non-coding regions of different genes. A short region of unknown sequence in the intron between the human J kappa and C kappa immunoglobulin coding regions was found to be sufficiently homologous to the corresponding segment of the mouse gene to form stable heteroduplexes. Although no specific function has yet been definitely ascribed to this region (which we call the kappa intron conserved region, or KICR), some functional significance has been inferred from the findings that (1) activation of B lymphocytes induces a DNase hypersensitivity site in this region and (2) deletions including this region reduce expression of kappa genes introduced into lymphoid cells. To delineate the KICR more precisely and to test the generality of the sequence conservation in a third species, we have sequenced this region of the human and mouse genes and have examined the corresponding region of a recently cloned rabbit kappa gene. We find a segment of about 130 base pairs (bp) that shows striking conservation in all three species, demonstrating homology significantly higher than within the C kappa coding region itself. Two short sequences from the J kappa-C kappa intron that were noted by other investigators to be homologous to proposed 'enhancer' sequences both lie within the conserved region.     

A hybrid recognition sequence in a recombinant restriction enzyme and the evolution of DNA sequence specificity

Early attempts to generate new restriction specificities by recombination between allelic restriction-modification systems have been unsuccessful. Bullas et al. succeeded in isolating a new specificity, SQ, in Salmonella that they interpreted as being the result of a recombination event between the parental strains, Salmonella typhimurium and S. postdam, which encode the SB and SP restriction systems, respectively. This interpretation has recently been confirmed by DNA heteroduplex studies with the SB, SP and SQ structural genes. We have determined the DNA sequences recognized by the SB and SP enzymes and found that, like all type I restriction sequences, they are split into two specific domains by a spacer of nonspecific sequence that, for both SB and SP, is 6 base pairs (bp) long. We have now determined the sequence recognized by the recombinant SQ enzyme and find that it is a hybrid between the SB and SP sequences, containing one specific domain from each parental strain. This result implies that each of the two specific domains is recognized by a physically distinct part of the enzyme.     

A membrane evolutionary algorithm for DNA sequence design in DNA computing

DNA sequence design has a crucial role in successful DNA computation,which has been proved to be an NP-hard(non-deterministic polynomial-time hard) problem.In this paper,a membrane evolutionary algorithm is proposed for the DNA sequence design problem.The results of computer experiments are reported,in which the new algorithm is validated and out-performs certain known evolutionary algorithms for the DNA sequence design problem.     

Evolution of genes and genomes on the Drosophila phylogeny

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.     

Interaction network containing conserved and essential protein complexes in Escherichia coli

Proteins often function as components of multi-subunit complexes. Despite its long history as a model organism, no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames (approximately 23% of the genome). A total of 857 proteins, including 198 of the most highly conserved, soluble non-ribosomal proteins essential in at least one bacterial species, were tagged successfully, whereas 648 could be purified to homogeneity and their interacting protein partners identified by mass spectrometry. An interaction network of protein complexes involved in diverse biological processes was uncovered and validated by sequential rounds of tagging and purification. This network includes many new interactions as well as interactions predicted based solely on genomic inference or limited phenotypic data. This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.     

Identification and nucleotide sequence of a diversity DNA segment (D) of immunoglobulin heavy-chain genes

A putative diversity segment of immunoglobulin heavy-chain genes (D segments) has been identified 700 base pairs 5' to JH1 DNA on the germ-line genome of the mouse. This 10-base pair D segment is flanked by two sets of sequences related to (SEE FORMULAR IN TEXT) which are possible recognition sites for a recombinase. The spacer separating the heptamer and the nonamer is 12 base pairs long on both sides of the D segment. As the space separating the two signal sequences in VH DNAs and JH DNAs is 23 +/- 1 base pairs long, the two recombinations required for creation of a complete immunoglobulin VH gene, a VH--D joining and a D--JH joining, follow a 12/23-base pair spacer rule. Allelic exclusion is discussed with respect to D segments.     

Complete replacement of mitochondrial DNA in Drosophila

The introduction of foreign mitochondria or mitochondrial DNA into a cell is a useful technique for clarifying the molecular mechanisms responsible for the maintenance of mitochondria. Novel combinations of mitochondrial and nuclear genomes have been studied in mammalian cells in culture and in yeast. In Drosophila, we have recently constructed heteroplasmic flies possessing both endogenous mitochondrial DNA and foreign mitochondrial DNA by intra- and interspecific transplantation of germ plasm. During the maintenance of these heteroplasmic lines, flies of D. melanogaster are produced that no longer possess their own mitochondrial DNA but retain the foreign mitochondrial DNA from D. mauritiana. .These flies are fertile and the foreign mitochondrial DNA is stably maintained in their offspring. Here we report the complete replacement of endogenous mitochondrial DNA with that from another multicellular species. Molecular and genetic analysis of this replacement in Drosophila should provide new insight into the functional interaction between nuclear and organelle genomes.     

Adaptive evolution of non-coding DNA in Drosophila

A large fraction of eukaryotic genomes consists of DNA that is not translated into protein sequence, and little is known about its functional significance. Here I show that several classes of non-coding DNA in Drosophila are evolving considerably slower than synonymous sites, and yet show an excess of between-species divergence relative to polymorphism when compared with synonymous sites. The former is a hallmark of selective constraint, but the latter is a signature of adaptive evolution, resembling general patterns of protein evolution in Drosophila. I estimate that about 40-70% of nucleotides in intergenic regions, untranslated portions of mature mRNAs (UTRs) and most intronic DNA are evolutionarily constrained relative to synonymous sites. However, I also use an extension to the McDonald-Kreitman test to show that a substantial fraction of the nucleotide divergence in these regions was driven to fixation by positive selection (about 20% for most intronic and intergenic DNA, and 60% for UTRs). On the basis of these observations, I suggest that a large fraction of the non-translated genome is functionally important and subject to both purifying selection and adaptive evolution. These results imply that, although positive selection is clearly an important facet of protein evolution, adaptive changes to non-coding DNA might have been considerably more common in the evolution of D. melanogaster.     

Hepatitis B virus DNA integration in a sequence homologous to v-erb-A and steroid receptor genes in a hepatocellular carcinoma

Hepatitis B virus (HBV) is clearly involved in the aetiology of human hepatocellular carcinoma (HCC) and the finding of HBV DNA integration into human liver DNA in almost all HCCs studied suggested that these integrated viral sequences may be involved in liver oncogenesis. Several HBV integrations in different HCCs and HCC-derived cell lines have been analysed after molecular cloning without revealing any obvious role for HBV. From a comparison of a HBV integration site present in a particular HCC with the corresponding unoccupied site in the non-tumorous tissue of the same liver, we now report that HBV integration places the viral sequence next to a liver cell sequence which bears a striking resemblance to both an oncogene (v-erb-A) and the supposed DNA-binding domain of the human glucocorticoid receptor and human oestrogen receptor genes. We suggest that this gene, usually silent or transcribed at a very low level in normal hepatocytes, becomes inappropriately expressed as a consequence of HBV integration, thus contributing to the cell transformation.