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D S Hogness

Publications and source records attributed to D S Hogness.

At least 55 records · Page 3Linked to original sources
PubMed1983

Molecular mapping of genetic and chromomeric units in Drosophila melanogaster.

We have used a set of overlapping cloned segments defining a 315 kb (X 10(3) base-pairs) region of Drosophila melanogaster chromosomal DNA to map the sequences associated with the polytene band-interbands (chromomeric units) and with the lethal complementation groups contained within this region. The molecular map positions of the 13 +/- 1 chromomeric units from the 87D5-6 to 87E5, 6 region of the third chromosome were determined by in situ hybridization of selected segments to the polytene chromosomes. The length of the largest chromomeric unit within the 315 kb region is approximately 160 kb, while that for the smallest is less than 7 kb and may be as short as 3 kb. By mapping the breakpoints of deletions within the 315 kb region, we have located its 12 lethal complementation groups, which include the genes coding for acetylcholinesterase (Ace) and xanthine dehydrogenase (rosy). Comparison of the two molecular maps indicates a one-to-one topographical correlation between the genetic and chromomeric units.

Animals↗
PubMed1983

Isolation, sequence analysis, and intron-exon arrangement of the gene encoding bovine rhodopsin.

We have isolated cDNA clones generated from the mRNA encoding the opsin apoprotein of bovine rhodopsin and used these cDNAs to isolate genomic DNA clones containing the complete opsin gene. Nucleotide sequence analysis of the cloned DNAs has yielded a complete amino acid sequence for bovine rhodopsin and provided an intron-exon map of its gene. The mRNA homologous sequences in the 6.4 kb gene consist of a 96 bp 5' untranslated region, a 1044 bp coding region, and a surprisingly long approximately 1400 bp 3' untranslated region, and are divided into five exons by four introns that interrupt the coding region. Secondary structure analysis predicts that the bovine rhodopsin chain, like that of bacteriorhodopsin, contains seven transmembrane segments. Interestingly, three of the four introns are immediately distal to the codons for three of these segments, and one of these introns marks the boundary between the C-terminal domain and a transmembrane domain.

Amino Acid Sequence↗
PubMed1982

Molecular organization of a Drosophila puff site that responds to ecdysone.

The 68C locus in the polytene chromosomes of Drosophila melanogaster salivary glands is puffed during the last half of the third larval instar and harbors the structural gene for sgs3, one of the glue polypeptides synthesized by the glands during this period. This puff regresses in response to the steroid hormone ecdysone. We have isolated a set of overlapping cloned segments that define approximately 50 kb of DNA at the 68C puff locus. Three polysomal poly(A)+ RNAs that are abundant in the salivary glands during the intermolt-puff stage are transcribed from three genes (II, III and IV) that map near the center of the cloned DNA in a 5 kb cluster region. These are the only transcripts from the 50 kb of 68C DNA detectable in these glands, and they are undetectable in other larval tissues at this stage, or in whole animals at other stages of development. Correlative criteria indicate that gene IV, which yields an RNA of 1.1 kb, is the structural gene for sgs3. Genes II and III, which yield RNAs of 0.36 kb and 0.32 kb, respectively, are oppositely oriented so that their promoters are adjacent, suggesting that this pair may form a single regulated unit, a suggestion that is enhanced by the fact that the pair is bounded by an inverted repeat of 0.3 kb elements. The possible, but as yet unidentified, functions of this gene pair are discussed. A 9.2 kb element belonging to a family of transposable elements called roo is inserted adjacent to the 5 kb cluster region in some but not other D. melanogaster strains. This insertion has no obvious effect on the transcription of genes II, III and IV. Although roo elements yield a 9 kb poly(A)+ RNA in embryos, no roo transcripts were detected in intermolt salivary glands, whether they do or do not contain an element at the 68C puff site.

Chromosome Mapping↗
PubMed1982

An expandable gene that encodes a Drosophila glue protein is not expressed in variants lacking remote upstream sequences.

The Drosophila melanogaster gene Sgs4 encodes one of the glue polypeptides, sgs-4, synthesized in the larval salivary gland. We have examined the structure and expression of Sgs4 in five strains that produce abundant amounts of sgs-4 and its mRNA and in four that do not. The nonproducers include three Japanese strains that accumulate trace amounts of mRNA and one strain, BER-1, that contains no detectable Sgs4 RNA. Sgs4 carries a tandem array of repeated 21 bp elements within its coding sequence. The number of elements per array varies, causing considerable differences in the lengths of Sgs4 and its mRNA among the strains. These differences in length are not correlated with differences in mRNA abundance; rather, the low or zero abundance in nonproducers correlates with the loss of DNA upstream from the gene. The Japanese nonproducers carry a 52 bp deletion 305 bp upstream from the 5' end of Sgs4, and BER-1 carries a 95 bp deletion 392 bp upstream. Curiously, each deletion encompasses one or more of the salivary-gland-specific DNAase I-hypersensitive sites which are known to flank the Sgs4 gene.

Animals↗
PubMed1980

A new high-capacity cosmid vector and its use.

The construction of a cosmid, MUA-3, designed for the convenient cloning of eukaryotic DNA segments up to 48 kb in length is described. The cosmid contains all of the plasmid pBR322 with approx. 400 bases of lambda DNA, including the cohesive end site, inserted at the pBR322 PstI endonuclease recognition site. Methods for using this vector to construct several types of Drosophila melanogaster genomic DNA libraries are given, and libraries made by these methods are characterized. A sheared Drosophila DNA-EcoRI linker library is shown to stably maintain average Drosophila DNA inserts of over 40 kb and up to 48 kb, and the efficiency of producing clones by a partial restriction and ligation method is shown to be over 3 X 10(5) clones/microgram of Drosophila DNA.

Bacteriophage lambda↗
PubMed1980

Molecular analysis of a gene in a developmentally regulated puff of Drosophila melanogaster.

An increase in the concentration of the steroid hormone ecdysone in late larval life triggers a profound change in the pattern of polytene chromosome puffs in the Drosophila melanogaster salivary gland. One of the preexisting puffs that regress as the ecdysone concentration increases is located at the 3C11-12 bands, the site of the Sgs-4 gene, which codes for the sgs-4 protein, one of the proteins in the salivary glue secretion. We have isolated cloned segments of chromosomal DNA that define a 60-kilobase region containing the 0.9-kilobase Sgs-4 gene, and we have determined its position and orientation within this region. Fine structure restriction endonuclease mapping shows that approximately 45% of this gene consists of tandemly repeated sequences of 21 base pairs that occupy most of its 5' half, indicating that most of the amino-terminal half of the sgs-4 protein consists of tandemly repeated amino acid sequences of seven residues. We also report on the amount of the Sgs-4 mRNA as a function of developmental stage and in nine different strains, four of which produce little or no sgs-4 protein. Three of the null strains produce minute amounts of the mRNA and one yields none, whereas the five sgs-4 producing strains yield abundant amounts. The mRNAs frm these strains exhibit different lengths, which correlate with different gene lengths that appear to result from different numbers of the repeated sequences in their tandem arrays.

Animals↗
PubMed1978

A novel arrangement of tandemly repeated genes at a major heat shock site in D. melanogaster.

Three cloned segments of Drosophila melanogaster DNA have been isolated that derive from the major heat shock site at 87C in chromosome 3. Each of these segments contains sequences homologous to a class of polysomal poly(A)+ RNAs whose synthesis is induced by heat shock of cultured cells. A combination of R loop, heteroduplex and restriction fragment maps of these segments reveals that their RNA-homologous sequences are arranged in tandemly repeated units, each unit consisting of an alpha element (0.49 kb) joined to a beta element (1.10 kb). The polysomal RNAs homologous to these alphabeta units (1.59 kb) are distributed into three size classes exhibiting approximate lengths of 1, 2 and 3 kb. R loop mapping demonstrated that the sequence of the 2 kb RNA is alphabetaalpha, indicating that it, and presumably the 3 kb RNA, derive from transcripts covering more than one repeated unit. One of the cloned segments contains a variant repeat unit, alphagamma, located between two alphabeta units. This unit has the same alpha element, but the beta element has been replaced by a nonhomologous gamma element (0.87 kb). Analysis of the total D. melanogaster DNA indicates that the 87C locus contains at least 21 tandemly repeated units, twelve of which were identified as alphabeta units and six as alphagamma units. The 21 or more units are distributed among at least three different tandem arrays separated by different spacer regions, one of which is within a cloned segment. Sequences in the gamma element, but not those in the alpha or beta elements, are also found at 87A, which contains another heat shock site. The possible roles of the alphabeta-type RNAs and of the gamma sequences are discussed in the light of these results.

Animals↗
PubMed1977

A novel arrangement of the 18S and 28S sequences in a repeating unit of Drosophila melanogaster rDNA.

The sequences corresponding to the 18S and 28S rRNAs have been mapped within a cloned 17 kilobase (kb) fragment formed by Eco R1 cleavage of Drosophila melanogaster rDNA. This fragment, Dm103, represents the longer of two major types of repeating units that are present in the rDNA of this fly, and was cloned as a hybrid plasmid, pDm103, consisting of Dm103 inserted at the Eco R1 site of the pSC101 vector (Glover et al., 1975). Mapping of the 18S and 28S rDNA in Dm103 was accomplished by quantitative determination of the amount of these rDNAs in each member of an ordered set of restriction fragments obtained by Hind III and Eco R1 ccleavage of pDm103. The amounts of 18S and 28S rDNAs were determined by hybridization of the rRNAs to fragments that were purified by cloning, and an unambiguous order of the fragments within pDm103 was established by heteroduplex mapping and from the stoichiometry of the fragment lengths. The resulting map revealed that the 4 kb of 28S rDNA within the long repeating unit represented by Dm103 is divided into two blocks that are separated by 5.4 kb of DNA of unknown function. It is this unusual arrangement of the 28S rDNA that distinguishes the long repeating units (17 kb) from the short units (11.5) kb), whose 4 kb of 28S rDna is confined to a single block, as is shown in the accompanying paper (White and Hogness, 1977). The remainder of the DNA in this long unit appears to be typically arranged, with the 2 kb of 18S rDNA confined to a single block that is separated by about 1 kb from the closest block of 28S rDNA.

Animals↗
PubMed1977

R loop mapping of the 18S and 28S sequences in the long and short repeating units of Drosophila melanogaster rDNA.

Cleavage of D. melanogaster rDNA with the Eco R1 restriction endonuclease reveals two major classes of repeating units: a long class of 17 kilobases (kb) and a short class of 11.4 kb. R loop mapping has been used to determine the topography of the sequences corresponding to the 18S and 28S rRNAs in both classes, including a cloned member (Dm103) of the long class. This mapping procedure derives from a novel reaction that we discovered between single-stranded RNA and homologous regions in duplex DNA molecules. In high formamide and at an elevated temperature, the RNA pairs with one of the two DNA strands in the region of homology to form an R loop in which one element is an RNA/DNA duplex and the other is single-stranded DNA (Figure 1). Mapping is accomplished by visualization of R loops in the electron microscope. The R loop map of Dm103 parallels that determined independently by Glover and Hogness (1977) from an analysis of its restriction fragments. Both maps indicate that the 28S rDNA in this cloned unit is divided into two blocks by a 5 kb insertion segment. R loop mapping of a population of long units obtained directly from the rDNA (that is, without cloning) has demonstrated that this interruption of the sequence coding for the 28S rRNA is a characteristic of the long class. By contrast, the 28S rDNA in the short units that we examined is not interrupted by an insertion segment. Otherwise, the R loop maps of the long and short units do not differ significantly. The two classes therefore correspond to repeating units that do (IN+) or do not (IN-) contain an insertion segment. Models for the transcription and function of these two classes of repeating units are discussed.

Animals↗
PubMed1977

Translation of Drosophila melanogaster sequences in Escherichia coli.

Thirty-seven independently cloned segments of Drosophila melanogaster DNA (Dm segments) were individually tested for their ability to promote the synthesis of new polypeptides in Escherichia coli K-12. The cloning vector was the pSC101 plasmid and the test system consisted of E. coli K-12 minicells that contained the hybrid pDm plasmids. Each of four pDm plasmids produced a new polypeptide, and one, pDm107, was selected for detailed mapping of the sequences required for the translation of its 38,000-dalton polypeptide, the Dm107 protein. Mapping was accomplished by constructing (i) deletion derivatives of pDm107 and (ii) new plasmids consisting of fragments of the Dm107 segment inserted into other vectors, and then testing these hybrids for their ability to promote the synthesis of the Dm107 protein, or truncated versions of this protein, in minicells. The 1000 base pairs of sequences that are translated to yield the Dm107 protein were thereby mapped at the center of the 18,000-base pair Dm107 segment, which consists of nonrepetitive sequences located at the base of the right arm of chromosome 2. The four polypeptides produced by the four pDm plasmids require sequences of 4000 base pairs for their translation, and the total amount of DNA in the 37 cloned Dm segments that were tested is approximately 400,000 base pairs. Because no new polypeptides were detected with the remaining 33 pDm plasmids, the fraction of D. melanogaster sequences that can be efficiently translated in E. coli K-12 is estimated to be 1 x 10(-2).

Animals↗
PubMed1975

Effect of heat shock on the synthesis of low molecular weight RNAs in drosophilia: accumulation of a novel form of 5S RNA.

The synthesis and stability of low molecular weight RNAs following heat shock in Drosophilia melanogaster cell cultures have been examined. When cultures are raised from 25 degrees C to 37 degrees C, the synthesis of tRNA and at least two other low molecular weight RNAs continues at the 25 degree C rate. 5.8S ribosomal RNA and most of the low molecular weight nuclear RNAs are not synthesized. The synthesis of 5S ribosomal RNA is greatly reduced. A large amount of an RNA of about 135 nucleotides in length accumulates at 37 degrees C. Nucleotide sequence analysis reveals that this RNA is a novel form of 5S RNA with approximately 15 additional nucleotides at its 3' end.

Base Sequence↗
PubMed1975

Characterization of six cloned DNAs from Drosophila melanogaster, including one that contains the genes for rRNA.

pDm plasmids were constructed from D. melanogaster and pSC101 DNAs by a modification of the EcoR1-ligase method which insured that each hybrid molecule contained a single segment of D. melanogaster chromosomal DNA (Dm segment). The sequences in the Dm segments of six cloned pDm DNAs were mapped within the D. melanogaster polytene chromosomes by in situ hybridization, and their repetition frequencies within the Dm segment and within the genome were determined. Four of these segments consist of sequences that are confined to single chromomeric regions in the polytene chromosomes and exhibit little or no repetition. The characteristics of this group, and also two of three Dm segments analyzed earlier (Wensink et al., 1974), are inconsistent with tandem repetition models of the chromomere. By contrast, the other two Dm segments contain moderately repetitive sequences that are located in the heterochromatin. One of these appears to be a segment of the Y chromosome in which about half the sequences are nonrepetitive and half are repeated about 33 times per genome, though they are not repeated within the segment. The second contains the DNA coding for 18 and 28S rRNA.

Animals↗
PubMed1975

Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene.

A method has been developed whereby a very large number of colonies of Escherichia coli carrying different hybrid plasmids can be rapidly screened to determine which hybrid plasmids contain a specified DNA sequence or genes. The colonies to be screened are formed on nitrocellulose filters, and, after a reference set of these colonies has been prepared by replica plating, are lysed and their DNA is denatured and fixed to the filter in situ. The resulting DNA-prints of the colonies are then hybridized to a radioactive RNA that defines the sequence or gene of interest, and the result of this hybridization is assayed by autoradiography. Colonies whose DNA-prints exhibit hybridization can then be picked from the reference plate. We have used this method to isolate clones of ColE1 hybrid plasmids that contain Drosophila melanogaster genes for 18 and 28S rRNAs. In principle, the method can be used to isolate any gene whose base sequence is represented in an available RNA.

DNA, Bacterial↗