A transposable element that splits the promoter region inactivates a Drosophila cuticle protein gene

Unraveling the Role of Cuticular Protein 3-like (HvCP3L) in the Chitin Pathway through RNAi and Methoxyfenozide Stress Response in Heortia vitessoides Moore

Cuticle proteins (CPs) constitute a multifunctional family; however, the physiological role of Cuticle Protein 3-like (CP3L) in Heortia vitessoides Moore remains largely unclear. In this study, we cloned the HvCP3L gene from the transcriptional library of Heortia vitessoides Moore. RT-qPCR results revealed that HvCP3L exhibited high expression levels during the larval stage of Heortia vitessoides Moore, particularly at the L5D1 stage, observed in both larval and adult heads. Through RNA interference, we successfully silenced the HvCP3L gene, resulting in a significant reduction in the survival rate of Heortia vitessoides Moore, with the survival rate from larvae to adults plummeting to a mere 17.7%, accompanied by phenotypic abnormalities. Additionally, we observed that the knockdown of HvCP3L led to the inhibition of genes in the chitin pathway. Following exposure to methoxyfenozide stress, the HvCP3L gene exhibited significant overexpression, coinciding with phenotypic abnormalities. These findings underscore the pivotal role of HvCP3L in the growth and development of Heortia vitessoides Moore.

An ungrouped cuticular protein is essential for normal endocuticle formation in the brown planthopper

Using transcriptome analysis of tissues of the brown planthopper (BPH), Nilaparvata lugens, we identified a gene tentatively designated NlCP21.92 that was expressed at high levels in the integument. Spatiotemporal expression profiling with quantitative PCR and Western blotting verified its integument-specific expression and showed periodic expression during molting. The open reading frame was GC-rich and encoded a hydrophobic polypeptide. The polypeptide contained AAPA/V repeat motifs and other sequence features similar to several reported cuticular proteins but lacked an R&R consensus and other chitin-binding domains. Double-stranded RNA-mediated RNA interference of the NlCP21.92 resulted in abnormal and lethal morphological phenotypes, and transmission electron microscopy revealed the corresponding ultrastructural defects. Immunohistochemical staining demonstrated that the NlCP21.92 protein was primarily located in the procuticle. Our results suggest that NlCP21.92 is a novel ungrouped cuticular protein essential for normal endocuticle formation.

Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster

Multiply inverted balancer chromosomes that suppress exchange with their homologs are an essential part of the Drosophila melanogaster genetic toolkit. Despite their widespread use, the organization of balancer chromosomes has not been characterized at the molecular level, and the degree of sequence variation among copies of balancer chromosomes is unknown. To map inversion breakpoints and study potential diversity in descendants of a structurally identical balancer chromosome, we sequenced a panel of laboratory stocks containing the most widely used X chromosome balancer, First Multiple 7 (FM7). We mapped the locations of FM7 breakpoints to precise euchromatic coordinates and identified the flanking sequence of breakpoints in heterochromatic regions. Analysis of SNP variation revealed megabase-scale blocks of sequence divergence among currently used FM7 stocks. We present evidence that this divergence arose through rare double-crossover events that replaced a female-sterile allele of the singed gene (sn(X2)) on FM7c with a sequence from balanced chromosomes. We propose that although double-crossover events are rare in individual crosses, many FM7c chromosomes in the Bloomington Drosophila Stock Center have lost sn(X2) by this mechanism on a historical timescale. Finally, we characterize the original allele of the Bar gene (B(1)) that is carried on FM7, and validate the hypothesis that the origin and subsequent reversion of the B(1) duplication are mediated by unequal exchange. Our results reject a simple nonrecombining, clonal mode for the laboratory evolution of balancer chromosomes and have implications for how balancer chromosomes should be used in the design and interpretation of genetic experiments in Drosophila.

Evolutionary age of repetitive element subfamilies and sensitivity of DNA methylation to airborne pollutants

Background

Repetitive elements take up >40% of the human genome and can change distribution through transposition, thus generating subfamilies. Repetitive element DNA methylation has associated with several diseases and environmental exposures, including exposure to airborne pollutants. No systematic analysis has yet been conducted to examine the effects of exposures across different repetitive element subfamilies. The purpose of the study is to evaluate sensitivity of DNA methylation in differentially‒evolved LINE, Alu, and HERV subfamilies to different types of airborne pollutants.

Methods

We sampled a total of 120 male participants from three studies (20 high-, 20 low-exposure in each study) of steel workers exposed to metal-rich particulate matter (measured as PM₁₀) (Study 1); gas-station attendants exposed to air benzene (Study 2); and truck drivers exposed to traffic-derived elemental carbon (Study 3). We measured methylation by bisulfite-PCR-pyrosequencing in 10 differentially‒evolved repetitive element subfamilies.

Results

High-exposure groups exhibited subfamily-specific methylation differences compared to low-exposure groups: L1PA2 showed lower DNA methylation in steel workers (P=0.04) and gas station attendants (P=0.03); L1Ta showed lower DNA methylation in steel workers (P=0.02); AluYb8 showed higher DNA methylation in truck drivers (P=0.05). Within each study, dose–response analyses showed subfamily-specific correlations of methylation with exposure levels. Interaction models showed that the effects of the exposures on DNA methylation were dependent on the subfamily evolutionary age, with stronger effects on older LINEs from PM₁₀ (p‒interaction=0.003) and benzene (p‒interaction=0.04), and on younger Alus from PM₁₀ (p-interaction=0.02).

Conclusions

The evolutionary age of repetitive element subfamilies determines differential susceptibility of DNA methylation to airborne pollutants.

Genomic organization of the cadmium-inducible tandem repeat 25-kDa metallothionein of the oligochaete worm Enchytraeus buchholzi

The terrestric oligochaete worm Enchytraeus buchholzi survives in cadmium (Cd)-polluted environments by aid of its Cd-inducible 25 kDa cysteine-rich protein (CRP). Here, we analyze promoter and structure of the crp gene and compare its relationship to MT genes. The crp gene, approximately 12 kbp long, consists of 10 exons with exons 2 to 9 encoding eight almost identical repeats of predominantly 31 amino acids of the CRP. The introns of the crp gene contain various repetitive elements including retrotransposon-like sequences. The 683-bp promoter of the non-constitutive crp gene exhibits a much higher basal activity than the mouse MT-II promoter in HepG2 cells. Essential for crp promoter activity is the distal region (-683/-521) with a GC box and the proximal region (-308/-8) with the four MREa, b, c, d and AP-1, -2, -3 elements, whereas the central portion (-521/-309) with CAAT box, CRE and a XRE causes promoter repression. The TATA box-, MREc- and the AP-2, -3-containing region are required for high crp promoter activity. Our data support the view that the crp gene is a unique MT-gene and has evolved by exon duplications from a MT-like ancestral gene.

A DROSOPHILA MELANOGASTER Strain From Sub-Equatorial Africa Has Exceptional Thermotolerance But Decreased Hsp70 Expression

Drosophila melanogaster collected in sub-equatorial Africa in the 1970s are remarkably tolerant of sustained laboratory culture above 30°C and of acute exposure to much warmer temperatures. Inducible thermotolerance of high temperatures, which in Drosophila melanogaster is due in part to the inducible molecular chaperone Hsp70, is only modest in this strain. Expression of Hsp70 protein and hsp70 mRNA is likewise reduced and has slower kinetics in this strain (T) than in a standard wild-type strain (Oregon R). These strains also differed in constitutive and heat-inducible levels of other molecular chaperones. The lower Hsp70 expression in the T strain apparently has no basis in the activation of the heat-shock transcription factor HSF, which is similar in T and Oregon R flies. Rather, the reduced expression may stem from insertion of two transposable elements, H.M.S. Beagle in the intergenic region of the 87A7 hsp70 gene cluster and Jockey in the hsp70Ba gene promoter. We hypothesize that the reduced Hsp70 expression in a Drosophila melanogaster strain living chronically at intermediate temperatures may represent an evolved suppression of the deleterious phenotypes of Hsp70.

Molecular structure of a functional Drosophila centromere

Centromeres play a critical role in chromosome inheritance but are among the most difficult genomic components to analyze in multicellular eukaryotes. Here, we present a highly detailed molecular structure of a functional centromere in a multicellular organism. The centromere of the Drosophila minichromosome Dp1187 is contained within a 420 kb region of centric heterochromatin. We have used a new approach to characterize the detailed structure of this centromere and found that it is primarily composed of satellites and single, complete transposable elements. In the rest of the Drosophila genome, these satellites and transposable elements are neither unique to the centromeres nor present at all centromeres. We discuss the impact of these results on our understanding of heterochromatin structure and on the determinants of centromere identity and function.

A quantitative analysis of modifier mutations which occur in mutation accumulation lines in Drosophila melanogaster

Seven enzyme activities were measured in Drosophila melanogaster lines in which spontaneous mutations had accumulated over about 300 generations under the minimum pressure of natural selection. These enzymes included alcohol dehydrogenase (ADH), alpha-glycerol-3-phosphate dehydrogenase (alpha GPDH), malate dehydrogenase (MDH), isocitrate dehydrogenase (IDH), glucose-6-phosphate dehydrogenase (G6PD), 6-phosphogluconate dehydrogenase (6PGD) and alpha-amylase (AMY). A significant genetic variance was observed for some enzyme activities. The mutations which alter the enzyme activities are called modifier mutations. The magnitudes of the genetic variance in modifier mutations differed greatly among enzymes but were often similar between two series of mutation accumulation lines (AW and JH). This may therefore indicate that the number of modifiers is specific for each enzyme system. The modifier mutation rate is suggested to be one of the clues for assessing the maintenance mechanism of protein polymorphism in natural populations.

Spatially regulated expression of retrovirus-like transposons during Drosophila melanogaster embryogenesis

Over twenty distinct families of long terminal direct repeat (LTR)-containing retrotransposons have been identified in Drosophila melanogaster. While there have been extensive analyses of retrotransposon transcription in cultured cells, there have been few studies of the spatial expression of retrotransposons during normal development. Here we report a detailed analysis of the spatial expression patterns of fifteen families of retrotransposons during Drosophila melanogaster embryogenesis (17.6, 297, 412, 1731, 3S18, blood, copia, gypsy, HMS Beagle, Kermit/flea, mdg1, mdg3, opus, roo/B104 and springer). In each case, analyses were carried out in from two to four wild-type strains. Since the chromosomal insertion sites of any particular family of retrotransposons vary widely among wild-type strains, a spatial expression pattern that is conserved among strains is likely to have been generated through interaction of host transcription factors with cis-regulatory elements resident in the retrotransposons themselves. All fifteen families of retrotransposons showed conserved patterns of spatially and temporally regulated expression during embryogenesis. These results suggest that all families of retrotransposons carry cis-acting elements that control their spatial and temporal expression patterns. Thus, transposition of a retrotransposon into or near a particular host gene-possibly followed by an excision event leaving behind the retrotransposon's cis-regulatory sequences-might impose novel developmental control on such a host gene. Such a mechanism would serve to confer evolutionarily significant alterations in the spatio-temporal control of gene expression.

A Drosophila melanogaster chromosome 2L repeat is expressed in the male germ line

We describe the initial characterisation of a Drosophila melanogaster locus, Mst40 (Male-specific transcript), that was cloned on the basis of its male-specific transcription during the third larval instar. Corresponding low molecular weight poly(A)+ mRNAs are abundant in primary spermatocytes, but in no other larval or adult tissue. During early embryogenesis Mst40 expression is complex; initially transcription is detected during early cleavage stages. This early expression appears as two discrete dots of hybridisation associated with each nucleus. Subsequently, the transcripts are abundant in the cytoplasm of the newly formed pole cells. In the genome Mst40 sequences are located in region 40, at the base of chromosome 2L, close to, or within, the beta-heterochromatin. The Mst40 sequences are organised as a tandemly arrayed 1.4 kb repeat unit. The repeat is conserved in all D. melanogaster strains examined but absent from other Drosophila species studied. The locus does not correspond to any known complementation groups in the region and has yet to be assigned a function.

A ubiquitin-conjugating enzyme, RAD6, affects the distribution of Ty1 retrotransposon integration positions

A galactose-inducible Ty1 element was used to generate 59 independent Ty1 inserts that inactivate the CAN1 gene. As found in previous studies, the distribution of these elements shows a gradient of insertion frequency from highest to lowest between the 5' and 3' ends of the gene. However, 53 independent Ty1 and Ty2 insertions isolated by an identical procedure in an isogenic rad6 deletion strain do not show this bias. In this strain, the Ty elements insert randomly throughout CAN1. These results show that the ubiquitin-conjugating enzyme, RAD6, alters the integration site preferences of Ty1 retrotransposons.

Preferential Y chromosomal location of TRIM, a novel transposable element of Drosophila miranda, obscura group

We have isolated a novel transposable element from the Y chromosome of Drosophila miranda (obscura group) which shows an organization intermediate between that of typical retroviruses and the I factor of Drosophila melanogaster. The site of integration of this element, TRIM, is an inverted repeat. On the 5' side the central region of TRIM is bordered by a sequence homologous to the tRNA primer binding site (PBS) and on the 3' side by a sequence homologous to the polypurine tract (PPT). The 5' LTR (long terminal repeat) contains transcription signals, such as a TATA box and a polyadenylation sequence. Three long open reading frames (ORFs) are found within the central region of the transposon. ORF1 and ORF2 show amino acid homology to the I factor of D. melanogaster and to conserved amino acid residues of retroviral reverse transcriptases. When used as a probe for in situ hybridization the TRIM element labels about 25 euchromatic sites and the chromocenter in polytene nuclei of D. miranda females. In the chromosome complement of males the polytenized part of the Y chromosome shows about the same number of additional TRIM homologous elements. Thus, as a result of this enrichment of TRIM elements in the Y chromosome, the genomic size of the TRIM population in D. miranda males is approximately doubled.

Mobile element insertions causing mutations in the Drosophila suppressor of sable locus occur in DNase I hypersensitive subregions of 5'-transcribed nontranslated sequences

The locations of 16 mobile element insertions causing mutations at the Drosophila suppressor of sable [su(s)] locus were determined by restriction mapping and DNA sequencing of the junction sites. The transposons causing the mutations are: P element (5 alleles), gypsy (3 alleles), 17.6, HMS Beagle, springer, Delta 88, prygun, Stalker, and a new mobile element which was named roamer (2 alleles). Four P element insertions occur in 5' nontranslated leader sequences, while the fifth P element and all 11 non-P elements inserted into the 2053 nucleotide, 5'-most intron that is spliced from the 5' nontranslated leader approximately 100 nucleotides upstream of the translation start. Fifteen of the 16 mobile elements inserted within a approximately 1900 nucleotide region that contains seven 100-200-nucleotide long DNase I-hypersensitive subregions that alternate with DNase I-resistant intervals of similar lengths. The locations of these 15 insertion sites correlate well with the roughly estimated locations of five of the DNase I-hypersensitive subregions. These findings suggest that the features of chromatin structure that accompany gene activation may also make the DNA susceptible to insertion of mobile elements.

Positive regulation of the Drosophila melanogaster G6PD gene by an insertion sequence

In a previous study, we have shown that the three high-G6PD activity mutants are characterized by insertion of the Ins1 sequence consisting of a core sequence flanked by two defective P elements (KP and KP'; the 32nd base of the KP was replaced by guanine in the KP') in front of exonI of the G6PD gene and that the sequence responsible for positive regulation of the G6PD gene expression might be the core sequence but not the flanking KP and KP' elements. The core sequence is composed of either one or two identical units in each mutant. In this report we present evidence (1) that insertion of the Ins1 sequence gives rise to overproduction of G6PD mRNA, (2) that the length and the 5' end of G6PD mRNA do not differ in wild-type and three mutants, (3) that the insertion site of the Ins1 sequence is the same in the mutants, and (4) that each unit of the core sequence has the same in the mutants, and (4) that each unit of the core sequence has a pair of DNase I-hypersensitive sites. The possibility exists that the binding of some regulatory proteins to the DNase I-hypersensitive sites might accelerate the transcription rate of the G6PD gene.

Regulation of larval cuticle protein gene expression in Drosophila melanogaster

Genes that encode 3rd instar larval cuticle proteins (LCP's) of Drosophila melanogaster are located in at least two chromosomal sites. The genes encoding four of the five predominant LCP's are located in a cluster at the chromosomal region 44D. They are organized in pairs that are transcribed divergently, and expressed with different timing during the third larval instar. Towards understanding the basis of gene regulation within the 44D cluster, we have analyzed genetic variants, including the 2-3 variant, which has an insertion of a copia-like transposable element, H.M.S. Beagle, within the 44D cluster. The Beagle element appears to inactivate the LCP-3 gene by inserting into its TATA box, but also may cause the precocious expression of two other LCP genes, LCP-1 and LCP-f2, in the cluster. The long terminal repeat (LTR) of the Beagle element apparently contains a sequence, perhaps an enhancer-like element, which causes altered expression of these genes. We have also investigated the cis-regulatory elements involved in expression of the LCP-2 gene in wild-type larvae. We have identified two upstream regions that may contain separate cis-regulatory elements. The region between -252 bp and -515 bp may be essential for any expression of LCP-2. Additionally, the region between -515 bp and -795 bp appears to be required for the normal level of expression of the LCP-2 gene.

Characterization of the AdhSL regulatory mutation in Drosophila melanogaster

We describe the characterization of a previously reported control mutation, AdhSL, in the alcohol dehydrogenase gene of Drosophila melanogaster, which results in decreased production of ADH molecules and subsequently lower ADH activity in adults. We find that the regulatory element modifies ADH mRNA levels and acts cis on both ADH protein and mRNA. It is not promoter specific but is developmentally specific to the adult stage. The AdhSL allele carries a 4.5-kb insert approximately 3 kb 5' to the distal promoter. This new insertion may be responsible for the regulatory phenotype of AdhSL.

Restriction of P-element insertions at the Notch locus of Drosophila melanogaster

P elements move about the Drosophila melanogaster genome in a nonrandom fashion, preferring some chromosomal targets for insertion over others (J. C. J. Eeken, F. H. Sobels, V. Hyland, and A. P. Schalet, Mutat. Res. 150:261-275, 1985; W. R. Engels, Annu. Rev. Genet. 17:315-344, 1983; M. D. Golubovsky, Y. N. Ivanov, and M. M. Green, Proc. Natl. Acad. Sci. USA 74:2973-2975, 1977; M. J. Simmons and J. K. Lim, Proc. Natl. Acad. Sci. USA 77:6042-6046, 1980). Some of this specificity may be due to recognition of a particular DNA sequence in the target DNA; derivatives of an 8-base-pair consensus sequence are occupied by these transposable elements at many different chromosomal locations (K. O'Hare and G. M. Rubin, Cell 34:25-36, 1983). An additional level of specificity of P-element insertions is described in this paper. Of 14 mutations induced in the complex locus Notch by hybrid dysgenesis, 13 involved P-element insertions at or near the transcription start site of the gene. This clustering was not seen in other transposable element-induced mutations of Notch. DNA sequences homologous to the previously described consensus target for P-element insertion are not preferentially located in this region of the locus. The choice of a chromosomal site for integration appears to be based on more subtle variations in chromosome structure that are probably associated with activation or expression of the target gene.

Restriction of P-element insertions at the Notch locus of Drosophila melanogaster

P elements move about the Drosophila melanogaster genome in a nonrandom fashion, preferring some chromosomal targets for insertion over others (J. C. J. Eeken, F. H. Sobels, V. Hyland, and A. P. Schalet, Mutat. Res. 150:261-275, 1985; W. R. Engels, Annu. Rev. Genet. 17:315-344, 1983; M. D. Golubovsky, Y. N. Ivanov, and M. M. Green, Proc. Natl. Acad. Sci. USA 74:2973-2975, 1977; M. J. Simmons and J. K. Lim, Proc. Natl. Acad. Sci. USA 77:6042-6046, 1980). Some of this specificity may be due to recognition of a particular DNA sequence in the target DNA; derivatives of an 8-base-pair consensus sequence are occupied by these transposable elements at many different chromosomal locations (K. O'Hare and G. M. Rubin, Cell 34:25-36, 1983). An additional level of specificity of P-element insertions is described in this paper. Of 14 mutations induced in the complex locus Notch by hybrid dysgenesis, 13 involved P-element insertions at or near the transcription start site of the gene. This clustering was not seen in other transposable element-induced mutations of Notch. DNA sequences homologous to the previously described consensus target for P-element insertion are not preferentially located in this region of the locus. The choice of a chromosomal site for integration appears to be based on more subtle variations in chromosome structure that are probably associated with activation or expression of the target gene.

Hsp28stl: a P-element insertion mutation that alters the expression of a heat shock gene in Drosophila melanogaster

We have identified and cloned a mutant allele of the small heat shock gene Hsp28 of Drosophila melanogaster. This allele, which we have called Hsp28stl, produces small amounts of a single aberrantly large, heat-inducible transcript in heat-shocked flies, while a normal-sized Hsp28 transcript is present only in fertile females. No Hsp28 transcript at all is detected in mutant prepupae, a stage when wildtype flies show high levels of Hsp28 RNA. We have cloned the Hsp28stl allele, and have found that a 1.3-kb defective P-element is present 5' to Hsp28 in the mutant line. The site of P-element insertion lies between the Hsp28 "TATA box" sequence and the Hsp28 RNA cap site; in contrast to previously described P-element insertions, the element at Hsp28stl is flanked by a two base pair duplication of the insertional target sequence. The results suggest that this insert may separate elements regulating heat-inducible and developmental expression of Hsp28, leading to the different patterns of transcription observed.

1731, a new retrotransposon with hormone modulated expression

We report here the characterisation of 1731, a new copia-like element of Drosophila melanogaster. 1731 was first isolated in a screening for ecdysterone modulated genes. This element is about 4.6 Kb long and is flanked by two long terminal repeats (LTRs) 336 base pairs in length. The whole 1731 element is transcribed into polyA+ RNAs, and these transcripts decrease rapidly upon hormonal treatment. 1731 is moderately repeated in the fly genome and slightly amplified in Kc/cells where extrachromosomal circular forms are found. The LTRs were sequenced in one cloned copy of 1731 and show a structural organisation similar to that of several other copia-like elements and retroviral proviruses. Small nucleotide stretches, similar to those found in Mouse Mammary Tumor Virus LTRs and known to be important in its regulation by a steroid hormone, occur in 1731 LTRs.

The cuticle proteins of Drosophila melanogaster: genetic localization of a second cluster of third-instar genes

Five third-instar larval cuticle protein genes are placed on the left arm of the third chromosome. For these five genes, 12 variants and two induced mutants are described. All the naturally occurring variants are codominant. One EMS-induced mutant is characterized by the codominant appearance of a new protein, and a second by a recessive mutation that codes for a modifier of third-instar larval cuticle protein 5 (L3CP-5). All but the putative modifier gene map to within less than 0.3 map units of each other on the left arm of the third chromosome at approximately 11. We propose that these genes constitute a cluster of third-instar cuticle protein genes. The induced recessive mutant maps outside of the cluster to a region also on the left arm of the third chromosome. The proteins and their genes should prove useful for both developmental and evolutionary studies.

P-element-induced control mutations at the r gene of Drosophila melanogaster

The P-M hybrid dysgenesis system was used to produce five putative regulatory mutations at the rudimentary locus, r. All five mutations were the result of insertions at the 5' end of the gene, upstream of the proposed start of transcription. All of the mutants displayed a leaky wing phenotype, and four of the mutants showed an uncoupling of the wing and female-sterility phenotypes, suggesting that they altered the normal spatial and temporal expression of the r gene. Four of the insertions were P elements. The fifth insertion, which was larger than an intact P element, consisted of a small P element connected to non-P-element DNA. Two of the mutants produced very little r transcript in adult females and were clustered 80 to 150 base pairs upstream of the start of transcription. The other three mutants had higher levels of r transcript in adult females and were clustered 440 to 500 base pairs upstream of the start of transcription. All of the data suggest that the insertions are in a 5' noncoding region of the r gene involved in the control of its spatial and temporal expression.

Hybrid dysgenesis-induced revertants of insertions at the 5' end of the rudimentary gene in Drosophila melanogaster: transposon-induced control mutations

Mutations in the 5' control region of the rudimentary (r) gene of Drosophila melanogaster were generated by using hybrid dysgenesis to mobilize P elements that were already inserted within this region. Eighteen new mutations out of 7793 chromosomes were isolated. Among the mutations were small insertions, deletions and inversions. All five of the deletions deleted into the 5' coding region of the r gene resulting in a severe mutant phenotype. The inversions and small insertions left the coding region intact, but altered the 5' control region. Northern analyses of the message levels in adult females indicated that these mutations alter the amount of the wild-type rudimentary message. These data also indicated that there is a region about 800 bp upstream of the start of transcription which is necessary for normal r expression. This region is not involved with the temporal and spatial regulation of r gene expression, but with the quantitative expression. An analysis of the DNA changes associated with each of the mutations demonstrates that P elements usually mobilize in an imprecise manner. Of the 22 mutations that have been isolated to date, only three are precise excisions. This means that P elements are potent mutators of the genome.

Nucleotide sequence characterization of a Drosophila retrotransposon, 412

The nucleotide sequence of the internal region of a Drosophila retrotransposon. 412, was determined. The genome of 412 was found to consist of two long open-reading frames (ORFs 1 and 2), an unusually long putative leader region and long terminal repeats (LTRs). As with 17.6, 297 and gypsy, ORFs 1 and 2 slightly overlap each other and are out of phase by +2. ORF2 includes the nucleotide sequences coding for the putative protease, reverse transcriptase and integrase, and is similar in entire organization to the pol gene of Moloney murine leukaemia virus. In spite of the difference in insertion specificity, integrase, an enzyme presumably responsible for insertion, was found to be similar in amino acid sequence to the counterparts of 17.6, 297 and gypsy. There is no ORF in 412 which corresponds to retroviral env or ORF3s of 17.6 and 297. Analysis of 412 transcripts suggested that 412 LTR is composed of U3, R and U5. The gene for a potential primer tRNA for putative reverse transcription of 412 was also surveyed and the 3'-terminal 15 nucleotides of a putative arginine tRNA were found to be exactly complementary to the putative primer-binding site of 412.

Identification of genes for reverse transcriptase-like enzymes in two Drosophila retrotransposons, 412 and gypsy; a rapid detection method of reverse transcriptase genes using YXDD box probes

Using synthetic oligonucleotides corresponding to the amino acid sequences best conserved among retroviral reverse transcriptases, we developed a rapid method to detect cloned DNA fragments with the genes for reverse transcriptases. By this technique followed by nucleotide sequence determination, nucleotide sequences coding for reverse transcriptase-like enzymes were identified in two Drosophila retrotransposons, gypsy and 412. Our sequence analysis suggested that there are at least two major groups of retrotransposons in Drosophila with respect to putative reverse transcriptases and both gypsy and 412 belong to a category of retrotransposons which have putative reverse transcriptases very similar in amino acid sequence to the counterpart of Moloney murine leukaemia virus, a typical mammalian retrovirus.

Identification and nucleotide sequence determination of a potential primer tRNA for reverse transcription of a Drosophila retrotransposon, 297

Drosophila retrotransposons have been shown to have genes for enzymes similar to the reverse transcriptase of retroviruse. They may possibly be involved in genome replication on translocation (15). Identification was made of a primer tRNA for the putative reverse transcription of a Drosophila retrotransposon, 297, and its genomic counterparts using a homology to the putative primer binding site of 297. Our nucleotide sequence analysis indicated a species of Drosophila serine tRNA to have two distinct properties similar to those characteristic of retroviral primer tRNA: its 3'terminal 18 nucleotides are exactly complementary to the putative primer binding site of 297 and its 19th base from the 3' end is modified. These results appear to support the notion stated above and suggest this serine tRNA to be the most likely candidate for a potential primer tRNA of 297.

Complete nucleotide sequence and genome organization of a Drosophila transposable genetic element, 297

The complete nucleotide sequence of 297, a Drosophila copia-like transposable element, was determined and compared with those of other similar Drosophila elements and mammalian retrovirus proviruses. It was found that 297 contains three long open reading frames, comparable in sizes and locations with gag, pol, and env genes in the proviruses of replication-competent retroviruses in vertebrates. The first and second open reading frames of 297 exhibit sequence homologies to gag and pol, respectively, of Moloney murine leukaemia virus. In particular, as with 17.6, another Drosophila copia-like element, the second open reading frame of 297 was shown to be very similar in its entire organization to the retroviral pol gene and to consist of three enzymatic domains. By contrast, no appreciable homology was found between the third open reading frame of 297 and the retroviral env gene. It is also suggested that 297 and 17.6 are a peculiar pair of copia-like elements recently diverged from a common progenitor.

P-element-induced control mutations at the r gene of Drosophila melanogaster

The P-M hybrid dysgenesis system was used to produce five putative regulatory mutations at the rudimentary locus, r. All five mutations were the result of insertions at the 5' end of the gene, upstream of the proposed start of transcription. All of the mutants displayed a leaky wing phenotype, and four of the mutants showed an uncoupling of the wing and female-sterility phenotypes, suggesting that they altered the normal spatial and temporal expression of the r gene. Four of the insertions were P elements. The fifth insertion, which was larger than an intact P element, consisted of a small P element connected to non-P-element DNA. Two of the mutants produced very little r transcript in adult females and were clustered 80 to 150 base pairs upstream of the start of transcription. The other three mutants had higher levels of r transcript in adult females and were clustered 440 to 500 base pairs upstream of the start of transcription. All of the data suggest that the insertions are in a 5' noncoding region of the r gene involved in the control of its spatial and temporal expression.

Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins

We have determined the complete nucleotide sequence of the copia element present at the white-apricot allele of the white locus in Drosophila melanogaster. This transposable element is 5,146 nucleotides long and contains a single long open reading frame of 4,227 nucleotides. Analysis of the coding potential of the large open reading frame, which appears to encode a polyprotein, revealed weak homology to a number of retroviral proteins, including a protease, nucleic acid-binding protein, and reverse transcriptase. Better homology existed between another part of the copia open reading frame and a region of the retroviral pol gene recently shown to be distinct from reverse transcriptase and required for the integration of circular DNA forms of the retroviral genome to form proviruses. Comparison of the copia sequence with those of the Saccharomyces cerevisiae transposable element Ty, several vertebrate retroviruses, and the D. melanogaster copia-like element 17.6 showed that Ty was most similar to copia, sharing amino acid sequence homology and organizational features not found in the other genetic elements.

Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins

We have determined the complete nucleotide sequence of the copia element present at the white-apricot allele of the white locus in Drosophila melanogaster. This transposable element is 5,146 nucleotides long and contains a single long open reading frame of 4,227 nucleotides. Analysis of the coding potential of the large open reading frame, which appears to encode a polyprotein, revealed weak homology to a number of retroviral proteins, including a protease, nucleic acid-binding protein, and reverse transcriptase. Better homology existed between another part of the copia open reading frame and a region of the retroviral pol gene recently shown to be distinct from reverse transcriptase and required for the integration of circular DNA forms of the retroviral genome to form proviruses. Comparison of the copia sequence with those of the Saccharomyces cerevisiae transposable element Ty, several vertebrate retroviruses, and the D. melanogaster copia-like element 17.6 showed that Ty was most similar to copia, sharing amino acid sequence homology and organizational features not found in the other genetic elements.

A 38 base pair insertion in the pro alpha 2(I) collagen gene of a patient with Marfan syndrome

Abnormalities in type I collagen have been recognized in a number of connective tissue disorders. In the Marfan syndrome, an autosomal dominant condition producing a generalized abnormality in connective tissue, no consistent abnormality has been identified, although one individual has been found to have an elongated pro alpha 2(I) collagen chain [Byers et al, Proc Natl Acad Sci USA 78:7745, 1981]. To determine the nature of the alteration in the gene that produced this abnormality, we studied the pro alpha 2(I) gene from this individual by genomic blotting and gene cloning. Genomic mapping studies detected no abnormalities. However, analysis of the cloned segment of the pro alpha 2(I) collagen gene from the Marfan individual indicates that the gene contains a 38 base pair insertion in an intron near the collagenase cleavage site. Although the relationship of this insertion to the protein abnormality is unclear, it may be a useful marker for the diagnosis of the Marfan syndrome.

Chromatin structure at the 44D larval cuticle gene locus in Drosophila: the effect of a transposable element insertion

The chromatin structure of the larval cuticle gene cluster at 44D was characterized in embryos from wild-type (Oregon R) and a variant line (2/3) of Drosophila melanogaster. A major DNase I hypersensitive (DH) site was found between genes II and III in the chromatin, in a position 5' to the transcriptional start of the genes in the cluster. The introduction of a 7.3 kilobase transposable element into the cluster in the 2/3 variant enhanced the sensitivity of the major site in 2/3 chromatin but had no other effect upon the pattern of DH sites associated with the wild-type sequences. The wild-type sequences were packaged into an ordered nucleosome-like array in embryos, as revealed by digestion with the chemical cleavage reagent (methidiumpropyl-EDTA) iron (II) [MPE . Fe(II)]. Nucleolytic cleavage within the transposable element chromatin shows it to be organized in an ordered array punctuated by several DH sites. While the patterns of DNase I hypersensitivity are similar in the vicinity of the direct terminal repeats, the patterns revealed by micrococcal nuclease and MPE . Fe(II) are not, indicating a different chromatin organization of these two identical sequences.

Sequence-specific insertion of the Drosophila transposable genetic element 17.6

As in the case of retrovirus proviruses, most of the Drosophila copia-like transposable elements so far examined are bounded by 5'TG...CA3' and inserted into the chromosome without obvious site-specificity. In the other copia-like elements, 297, HMS Beagle and 17.6 (refs 5-7), terminal dinucleotides (5'TG...CA3') are completely absent and, instead, 5'(A)GT is present at least at one of the termini. One important feature of these three elements may be frequent insertion into 'TATA' boxes, since the three of four insertion sites so far examined were TATA boxes, two for H3 histone genes and one for a cuticle gene. Because of the importance of this type of insertion, we extensively analysed site-specificity using 17.6 as a model. Our results, described here, suggest that insertion of 17.6 takes place in a site-specific fashion, using a target 5'ATAT corresponding to the major portion of the consensus TATA box, TATAATAAT.

Insertion of retrovirus into the first intron of alpha 1(I) collagen gene to embryonic lethal mutation in mice

Integration of the Moloney murine leukemia virus (M-MuLV) into the germ line of Mov-13 mice blocked formation of stable alpha 1(I) collagen mRNA and led to an embryonic lethal mutation. A 14-kilobase fragment representing the integration site of the virus was molecularly cloned and identified as the alpha 1(I) collagen gene. Sequence and nuclease S1 mapping analyses were performed to characterize the position of the proviral genome in relation to the transcriptional map of the mutated gene. The results indicated that the virus has inserted into the first intron 19 base pairs downstream of the intron/exon boundary. Sequence comparison showed a striking homology of exon sequences and sequences up to 215 base pairs upstream of the mRNA start between the mouse and the human alpha 1(I) collagen gene. This indicates that the sequences upstream of the mRNA start are highly conserved during evolution, suggesting that this region has an important role in the control of tissue-specific collagen expression.

Preferential integration of yeast transposable element Ty into a promoter region

Mobile genetic elements have been identified in several eukaryotic organisms and some classes have been found to share common structural features with the proviral forms of animal retroviruses. The representatives of this class of mobile elements in the yeast Saccharomyces cerevisiae are called Ty elements, which could be a useful model system for studying the transposition of retrovirus-like elements. Here we have attempted to answer two questions often raised in discussions of the biological importance of transposition: what is the frequency of spontaneous Ty transposition, and are there certain chromosomal regions into which Ty elements preferentially integrate? We chose the LYS2 gene to investigate these questions because it allows direct selection of both mutants and revertants. We have found that 2% of spontaneous lys2 mutants are caused by Ty transposition with a preferential integration into the transcription initiation region.

Analysis of DNA structural patterns and sequence organization at the larval cuticle locus in Drosophila melanogaster

We examined the pattern of DNA organization at the larval cuticle gene complex 44D of Drosophila melanogaster, using micrococcal nuclease and the 1,10-phenanthroline-cuprous complex. The initial cleavage patterns obtained with both reagents exhibited "gaps" at the positions of each of the genes examined, as well as at a pseudogene sequence contained within the complex. An additional gap for which no gene exists was observed for both patterns. The cleavage pattern obtained with micrococcal nuclease was unaltered, at a level of resolution of +/- 50 base pairs, in a mutant containing a transposable element. Analysis of the sequence data from this 5.5-kilobase gene cluster indicated that the sequence per se, and not the general base composition, is a dominant factor in determining the patterns observed.

A DNA insertion in the apolipoprotein A-I gene of patients with premature atherosclerosis

Apolipoprotein A-I (apo A-I) is the major protein constituent of high-density lipoprotein (HDL). The study of the apo A-I gene is of interest because plasma levels of HDL have been inversely correlated with the development of coronary artery disease and because polymorphisms related to this gene have been associated with hypertriglyceridaemia and premature atherosclerosis. We have recently isolated and characterized the human apo A-I gene and have shown that apo A-I and apolipoprotein C-III (apo C-III) genes are physically linked and that a polymorphism (of unknown frequency in the general population) of the apo A-I gene is inherited as a mendelian trait linked to premature atherosclerosis in an affected family (not the same polymorphism as has previously been reported to be associated with hypertriglyceridaemia). Here we report that this polymorphism is due an at least 6.5-kilobase (kb) DNA insertion in the coding region of the apo A-I gene and that there is no detectable alteration (as determined by limited genomic blotting analysis) of the apo C-III gene of these patients.

Analysis of DNA structural patterns and sequence organization at the larval cuticle locus in Drosophila melanogaster

We examined the pattern of DNA organization at the larval cuticle gene complex 44D of Drosophila melanogaster, using micrococcal nuclease and the 1,10-phenanthroline-cuprous complex. The initial cleavage patterns obtained with both reagents exhibited "gaps" at the positions of each of the genes examined, as well as at a pseudogene sequence contained within the complex. An additional gap for which no gene exists was observed for both patterns. The cleavage pattern obtained with micrococcal nuclease was unaltered, at a level of resolution of +/- 50 base pairs, in a mutant containing a transposable element. Analysis of the sequence data from this 5.5-kilobase gene cluster indicated that the sequence per se, and not the general base composition, is a dominant factor in determining the patterns observed.