Use of a cDNA library for studies on evolution and developmental expression of the chorion multigene families

Gene Expression Analyses of Mutant Flammulina velutipes (Enokitake Mushroom) with Clogging Phenomenon

Regulation of proper gene expression is important for cellular and organismal survival, maintenance, and growth. Abnormal gene expression, even for a single critical gene, can thwart cellular integrity and normal physiology to cause diseases, aging, and death. Therefore, gene expression profiling serves as a powerful tool to understand the pathology of diseases and to cure them. In this study, the difference in gene expression in Flammulina velutipes was compared between the wild type (WT) mushroom and the mutant one with clogging phenomenon. Differentially expressed transcripts were screened to identify the candidate genes responsible for the mutant phenotype using the DNA microarray analysis. A total of 88 genes including 60 upregulated and 28 downregulated genes were validated using the real-time quantitative PCR analysis. In addition, proteomic differences between the WT and mutant mushroom were analyzed using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). Interestingly, the genes identified by these genomic and proteomic analyses were involved in stress response, translation, and energy/sugar metabolism, including HSP70, elongation factor 2, and pyruvate kinase. Together, our data suggest that the aberrant expression of these genes attributes to the mutant clogging phenotype. We propose that these genes can be targeted to foster normal growth in F. velutipes.

Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research

In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.

Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects

Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.

The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis

As one of the most widespread metabolic diseases, atherosclerosis affects nearly everyone as they age; arteries gradually narrow from plaque accumulation over time reducing oxygenated blood flow to central and periphery causing heart disease, stroke, kidney problems, and even pulmonary disease. Personalized medicine promises to bring treatments based on individual genome sequencing that precisely target the molecular pathways underlying atherosclerosis and its symptoms, but to date only a few genotypes have been identified. A promising alternative to this genetic approach is the identification of pathways altered in atherosclerosis by transcriptome analysis of atherosclerotic tissues to target specific aspects of disease. Transcriptomics is a potentially useful tool for both diagnostics and discovery science, exposing novel cellular and molecular mechanisms in clinical and translational models, and depending on experimental design to identify and test novel therapeutics. The cost and time required for transcriptome analysis has been greatly reduced by the development of next generation sequencing. The goal of this resource article is to provide background and a guide to appropriate technologies and downstream analyses in transcriptomics experiments generating ever-increasing amounts of gene expression data.

A decade of RNA virus metagenomics is (not) enough

It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.

Transcriptomics technologies

Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst noncoding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline. Transcriptomics has been defined by repeated technological innovations that transform the field. There are two key contemporary techniques in the field: microarrays, which quantify a set of predetermined sequences, and RNA sequencing (RNA-Seq), which uses high-throughput sequencing to capture all sequences. Measuring the expression of an organism's genes in different tissues, conditions, or time points gives information on how genes are regulated and reveals details of an organism's biology. It can also help to infer the functions of previously unannotated genes. Transcriptomic analysis has enabled the study of how gene expression changes in different organisms and has been instrumental in the understanding of human disease. An analysis of gene expression in its entirety allows detection of broad coordinated trends which cannot be discerned by more targeted assays.

Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules

Background

Computational approaches toward gene annotation are a formidable challenge, now that many genome sequences have been determined. Each gene has its own function, but complicated cellular functions are achieved by sets of genes. Therefore, sets of genes with strong functional relationships must be identified. For this purpose, the similarities of gene expression patterns and gene sequences have been separately utilized, although the combined information will provide a better solution.

Result & Discussion

We propose a new method to find functional modules, by comparing gene coexpression profiles among species. A coexpression pattern is represented as a list of coexpressed genes with each guide gene. We compared two coexpression lists, one from a human guide gene and the other from a homologous mouse gene, and defined a measure to evaluate the similarity between the lists. Based on this coexpression similarity, we detected the highly conserved genes, and constructed human gene networks with conserved coexpression between human and mouse. Some of the tightly coupled genes (modules) showed clear functional enrichment, such as immune system and cell cycle, indicating that our method could identify functionally related genes without any prior knowledge. We also found a few functional modules without any annotations, which may be good candidates for novel functional modules. All of the comparisons are available at the http://v1.coxsimdb.info web database.

History of retinoic acid receptors

The discovery of retinoic acid receptors arose from research into how vitamins are essential for life. Early studies indicated that Vitamin A was metabolized into an active factor, retinoic acid (RA), which regulates RNA and protein expression in cells. Each step forward in our understanding of retinoic acid in human health was accomplished by the development and application of new technologies. Development cDNA cloning techniques and discovery of nuclear receptors for steroid hormones provided the basis for identification of two classes of retinoic acid receptors, RARs and RXRs, each of which has three isoforms, α, β and ɣ. DNA manipulation and crystallographic studies revealed that the receptors contain discrete functional domains responsible for binding to DNA, ligands and cofactors. Ligand binding was shown to induce conformational changes in the receptors that cause release of corepressors and recruitment of coactivators to create functional complexes that are bound to consensus promoter DNA sequences called retinoic acid response elements (RAREs) and that cause opening of chromatin and transcription of adjacent genes. Homologous recombination technology allowed the development of mice lacking expression of retinoic acid receptors, individually or in various combinations, which demonstrated that the receptors exhibit vital, but redundant, functions in fetal development and in vision, reproduction, and other functions required for maintenance of adult life. More recent advancements in sequencing and proteomic technologies reveal the complexity of retinoic acid receptor involvement in cellular function through regulation of gene expression and kinase activity. Future directions will require systems biology approaches to decipher how these integrated networks affect human stem cells, health, and disease.

Linkage and homology analysis divides the eight genes for the small subunit of petunia ribulose 1,5-bisphosphate carboxylase into three gene families

Twenty-six lambda phage clones with homology to coding sequences of the small subunit (SSU) of ribulose 1,5-bisphosphate carboxylase have been isolated from an EMBL3 lambda phage bank of Petunia (Mitchell) DNA. Restriction mapping of the phage inserts shows that the clones were obtained from five nonoverlapping regions of petunia DNA that carry seven SSU genes. Comparison of the HindIII genomic fragments of petunia DNA with the HindIII restriction fragments of the isolated phage indicates that petunia nuclear DNA encodes eight SSU genes, seven of which are present in the phage clones. Two incomplete genes, which contain only the 3' end of an SSU gene, were also found in the phage clones. We demonstrate that the eight SSU genes of petunia can be divided into three gene families based on homology to three petunia cDNA clones. Two gene families contain single SSU genes and the third contains six genes, four of which are closely linked within petunia nuclear DNA.

UV-induction of chalcone synthase mRNA in cell suspension cultures of Petroselinum hortense

DNAs complementary to poly(A)(+) mRNAs from UV-irradiated cell suspension cultures of parsley (Petroselinum hortense) were inserted into pBR322 and used to transform Escherichia coli strain RR1. A clone containing a DNA complementary to chalcone synthase mRNA was identified by hybrid-selected and hybrid-arrested translation. Large and rapid changes in the amount of chalcone synthase mRNA in response to irradiation of the cells was detected by RNA blot hybridization experiments. The pattern of changes coincided with that previously determined for the rate of chalcone synthase synthesis as measured either in vivo or with polyribosomal mRNA in vitro. The results are consistent with the hypothesis that induction of chalcone synthase by UV light is due to a transient increase in the rate of synthesis of chalcone synthase mRNA.

Gene profiling techniques and their application in angiogenesis and vascular development

The analysis of gene expression in specific tissues and physiological processes has evolved over the last 20 years from the painstaking identification of selected genes to the relatively efficient and open-ended surveying of potentially all genes expressed in a tissue. Current art for gene discovery includes the use of large-scale arrays of cDNA sequences or oligonucleotides, and molecular 'tagging' techniques such as GeneCalling and SAGE. Common to each of these techniques is a reliance on the increasingly comprehensive databases of human and mouse EST and full-length gene sequences. Early efforts to characterize candidate genes were limited by their narrow scope, while current efforts are confounded by the enormous volume of data returned. Sophisticated software tools are an integral part of the analysis, helping to organize information into coherent groups with temporal or functional similarity. These techniques, in conjunction with the continued analysis of human genetic syndromes, transgenic, and knockout mice, have driven genetic analysis of angiogenesis and vascular development from describing which individual genes are involved to defining the outlines of regulatory networks.

Transgenic mouse model of AA amyloidosis

AA amyloidosis can be induced in mice experimentally through injection of certain chemical or biological compounds. However, the usefulness of this approach is limited by its dependence on exogenous inflammatory agents that stimulate cytokines to increase the synthesis of precursor serum amyloid A (SAA) protein and the transitory nature of the pathological fibrillar deposits. We now report that transgenic mice carrying the human interleukin 6 gene under the control of the metallothionein-I promoter had markedly increased concentrations of SAA and developed amyloid in the spleen, liver, and kidneys by 3 months of age. At the time of death about 6 months later, organs obtained from these animals had extensive amyloid deposits. This disease process was apparent radiographically using small-animal computer axial tomography and magnetic resonance imaging equipment. The AA nature of the amyloid was evidenced immunohistochemically and was unequivocally established by sequence analysis of protein extracted from the fibrils. The availability of this unique in vivo experimental model of AA amyloidosis provides the means to assess the therapeutic efficacy of agents designed to reduce or prevent the fibrillar deposits found in AA and other types of amyloid-associated disease.

Linkage and evolutionary diversification of developmentally regulated multigene families: tandem arrays of the 401/18 chorion gene pair in silkmoths

The coordinately expressed silkmoth chorion genes, 401 and 18, are closely linked as a pair, in divergent orientation. Analysis of overlapping clones (chromosomal "walk") demonstrated that each of the multiple copies of this gene pair is embedded within a larger deoxyribonucleic acid unit, which is tandemly repeated in a few arrays or possibly a single array. Southern analysis and examination of clones from a single individual moth demonstrated that the repeat units are extensively polymorphic in restriction sites, length, and possibly number, no differential amplification was evident during choriogenesis. Intron and 5'-flanking sequences were shown to be specific for the 401/18 gene pair and not to be present elsewhere in the genome. The spatial distribution of variations in the genes and their flanking sequences were examined.

Transgenic regulation of moth chorion gene promoters in Drosophila: tissue, temporal, and quantitative control of four bidirectional promoters

Bidirectional chorion gene promoter regions from three silkmoth species, Bombyx mori, Antheraea pernyi, or Antheraea polyphemus (members of two different moth families), were tested for their ability to transcriptionally activate a bacterial marker gene (chloramphenicol acetyltransferase) in transformant Drosophila. Relatively short 5' flanking DNA fragments (272-367 bp) of chorion gene pairs are sufficient to confer a high degree of tissue and choriogenic stage specificity of expression to the marker gene. Thus, significant conservation of molecular interactions controlling transcription during choriogenesis is observed between the distantly related orders, Lepidoptera and Diptera. However, quantitative and fine temporal regulation in the Drosophila host does not fully parallel the in situ regulation in moths, indicating that some regulatory protein-DNA interactions have diversified in the approximately 250 million years since the last common ancestor of these insect groups. Limited in vitro mutagenesis of a B. mori promoter DNA has shown that a central 189-bp region includes elements sufficient for the qualitative specificity of chorion-specific expression. The same experiments have shown that a previously identified essential element, centered on the TCACGT hexamer, is not sufficient for chorion-specific expression: an additional essential element or elements are found farther upstream, within a 112-bp DNA region. Comparisons of silkmoth and Drosophila chorion gene promoter sequences have identified some candidates for cis-acting elements involved in the developmental regulation of chorion gene expression.

Morphogenesis of silkmoth chorion: sequential modification of an early helicoidal framework through expansion and densification

The silkmoth chorion is a helicoidally layered, fibrous structure which is constructed in four sequential morphogenetic modes, beginning with the assembly of a thin, low density lamellar framework. Subsequently, the framework expands in height by the insertion of additional fiber sheets into the preexisting lamellae. This expansion mode begins farthest from the follicular secretory cells and progresses in reverse. Individual fibers then grow in thickness, presumably through accretion of newly synthesized proteins, and eventually fuse. This third mode, which also begins in the most distant lamellae and proceeds in reverse, is called densification, as it results in an approximately two fold increase in overall chorion density without further lamellar expansion. Finally, lamellogenesis is recapitulated in miniature in a region of the chorion's surface, where very-late-forming lamellae are molded into prominent surface structures, the aeropyle crowns. The densification and especially the expansion modes suggest considerable fluidity in the developing chorion, consistent with its proposed cholesteric liquid crystalline structure. Such a structure is also consistent with numerous deviations from the ideal helicoidal array. These distortions and defects are described and discussed in terms of their possible origin and function.

Evolution of chorion structural genes and regulatory mechanisms in two wild silkmoths: a preliminary analysis

We report a preliminary analysis of structural and regulatory evolution of the A and B chorion gene families in two wild silkmoths, Antheraea pernyi and Antheraea polyphemus. Homospecific and heterospecific dot hybridizations were performed between previously characterized A. polyphemus complementary DNA clones and total or stage-specific follicular mRNAs from the two species. The hybridization patterns indicated substantial interspecies changes in the abundance of corresponding mRNA sequences (heteroposic evolution) without substantial changes in their developmental specificities (heterochronic evolution). In addition, the proteins encoded in the two species by corresponding mRNAs were determined by hybrid-selected translation followed by electrophoretic analysis. The results suggested that the proteins evolve in size, presumably through internal deletions and duplications.

Isolation and preliminary characterisation of cDNA clones representing mRNAs associated with tumour progression and metastasis in colorectal cancer

We have constructed cDNA libraries from the poly(A)+ RNA of normal colonic mucosa and a liver metastasis from a colonic adenocarcinoma. Differential screening of these libraries using 32P-labelled cDNAs transcribed from poly(A)+ RNAs isolated from specimens of four normal colonic mucosae, five adenocarcinomas, and three liver metastases by Grunstein-Hogness and dot-blot hybridization has identified a number of recombinant cDNA clones homologous to mRNAs that appear to differ significantly in abundance between normal and neoplastic colon and metastases. These cDNA clones, and others identified in the libraries, may be of considerable importance both as diagnostic tools and in defining the phenotypic changes associated with tumour progression and metastasis.

Developmental and tissue-specific regulation of beta-tubulin gene expression in the embryo of the sea urchin Strongylocentrotus purpuratus

Four beta-tubulin mRNAs in the embryo of the sea urchin Strongylocentrotus purpuratus are transcribed from at least 3 of the 9-12 beta-tubulin genes. A beta 1 tubulin mRNA of 1.8 kb, transcribed from a unique beta 1 gene, is expressed with high specificity in the pluteus ectoderm. Another 1.8-kb mRNA, beta 2, and a 2.5-kb beta 3 mRNA are moderately ectoderm specific. In contrast, a 3.0-kb beta 4 mRNA is highly specific for the endomesoderm tissue fraction. Certain similarities in developmental and tissue-specific expression suggest that these beta-tubulin genes may be related in their mode of regulation to counterparts among the genes for actin, another cytoskeletal protein. Measurements of absolute amounts revealed a distinct developmental profile for each beta-tubulin mRNA. An increase in the total amount of beta-tubulin mRNA in the early blastula was correlated with an increase in transcription rate per nucleus; whereas, later in the mesenchyme blastula stage, the beta-tubulin mRNA level decreased sharply as the rate of beta-tubulin gene transcription on a per embryo basis remained constant. Thus, during development through the blastula stages, there was a switch to a predominantly posttranscriptional regulation of beta-tubulin mRNA expression, probably through a decrease in mRNA stability.

The occurrence of Ds-like sequences in cereal genomes

The occurrence of DNA sequences similar to the Ds-element of sh-m5933 maize (Ds-like sequences) was studied in other representatives of the Gramineae. The approximate number of copies of such sequences found under gentle and stringent conditions of washing was determined by dot-hybridization. It was shown that in the maize genome the number of copies of Ds-like sequences exceeds about ten-fold the content of such sequences found in wheat, rye and barley genomes. Quantitative differences in Ds-like sequences between wheat species with various genomes and ploidies (when estimated per genome) as well as between different H. vulgare varieties was not determined. The various melting points (Tm) of DNA-duplexes formed when the Ds-element is hybridized with wheat, rye and barley DNA respectively do not show significant differences and are essentially lower than the Tm of the Ds-element (by 8°-9°C). Thus, these duplexes have 9-11% of nucleotide substitutions in comparison to Ds sh-m5933. The data obtained permit one to suppose the presence of a series of Ds-like sequences heterogenous for the length and degree of homology to the Ds-element isolated from the shrunken locus (sh-m5933) of maize DNA.

Organization of regionally expressed silkmoth chorion genes

We described the organization of two silkmoth chorion genes, called E1 and E2, whose expression is largely restricted in time to the very late period of choriogenesis and in space to one of two major subpopulations of follicle cells. Using E1 and E2 clone cDNAs as probes, we showed that gene copy numbers per haploid genome remain constant throughout silkmoth development despite major changes in total DNA content per nucleus. Furthermore, gene copy numbers are the same in both cellular regions of the choriogenic follicle despite differences in nuclear size and levels of E gene expression. Southern analysis indicated between two and four copies each for E1 and E2 genes. Analysis of chromosomal clones showed that single copies of E1 and E2 are separated by about 7.5 kilobases and are transcribed from the same DNA strand. Two distinct pairs of cloned E1 and E2 genes were characterized. No other chorion genes were in their immediate vicinity.

Patterns of region-specific chorion gene expression in the silkmoth and identification of shared 5' flanking genomic elements

Time-dependent and cell-specific changes in concentrations of total RNA, of poly A+ RNA, and of specific mRNAs have been measured throughout silkmoth choriogenesis. Levels of total RNA and of poly A+ RNA are maintained throughout much of choriogenesis, but decrease at least fourfold during the very late period, in parallel with a decrease in overall protein synthesis. Very late period changes in total RNA and in poly A+ RNA are less pronounced in the aeropyle crown region, where a subset of chorion proteins is preferentially synthesized, than in the flat region. Maximal accumulation of the E1 and E2 chorion mRNAs occurs preferentially in the aeropyle crown region during the very late period. Uridine pulse-labeling studies suggest that E1 and E2 transcription is similarly aeropyle crown region-specific and immediately precedes the time of maximal E1 and E2 RNA accumulation and protein synthesis. Sequences from the 5' flanking regions of E1 and E2 genes have been compared. Several oligonucleotide sequences are present in both genes, and some are duplicated. These are potential cis-acting, regulatory elements.

Organization of regionally expressed silkmoth chorion genes

We described the organization of two silkmoth chorion genes, called E1 and E2, whose expression is largely restricted in time to the very late period of choriogenesis and in space to one of two major subpopulations of follicle cells. Using E1 and E2 clone cDNAs as probes, we showed that gene copy numbers per haploid genome remain constant throughout silkmoth development despite major changes in total DNA content per nucleus. Furthermore, gene copy numbers are the same in both cellular regions of the choriogenic follicle despite differences in nuclear size and levels of E gene expression. Southern analysis indicated between two and four copies each for E1 and E2 genes. Analysis of chromosomal clones showed that single copies of E1 and E2 are separated by about 7.5 kilobases and are transcribed from the same DNA strand. Two distinct pairs of cloned E1 and E2 genes were characterized. No other chorion genes were in their immediate vicinity.

Gene regulation and evolution in the chorion locus of Bombyx mori. Structural and developmental characterization of four eggshell genes and their flanking DNA regions

We report on the detailed structural and developmental characterization of four chorion genes and a truncated pseudogene located within a 9.5 X 10(3) base chromosomal segment. These genes belong to the A and B multigene families and, like previously characterized moth chorion genes, are arranged in tightly linked pairs, which are divergently transcribed (A/B.L11 and A/B.L12). On the basis of their high degree of sequence divergence, the A genes define two distinct subfamilies, while the more homologous B genes represent different copies of the same gene type. The A.L11 and B.L11 introns are much longer, in each case because of a single inserted DNA segment that is missing from A.L12 or B.L12. The 2.1 X 10(3) base insertion in A.L11 is the first retrovirus-like transposable element characterized in Bombyx mori. The very short 5' flanking sequences of A/B.L11 and A/B.L12 (277 and 276 base-pairs) are distinct as shown by hybridization but both recur in additional chorion gene pairs, forming two respective classes that are expressed during distinctly different developmental periods. The divergently transcribed genes of each pair, which border the same 5' flanking sequence, are expressed co-ordinately, during the same developmental period. Detailed comparisons of the 5' flanking regions, and of the corresponding region of the Drosophila s15-1 chorion gene, revealed numerous, very short sequence elements that are shared. One such element, T-C-A-C-G-T, is also associated with all five sequenced Drosophila chorion genes. Some elements are repeated in a dyad symmetrical pattern, i.e. are associated with each of the two genes in a pair, while others, including T-C-A-C-G-T, occur only once per 5' flanking region, and, if functionally important, would presumably act bi-directionally on both genes of the pair.

Stage-specific patterns of collagen gene expression during development of Caenorhabditis elegans

Collagens are the major protein components of the Caenorhabditis elegans cuticle and are encoded by a large family of 40 to 150 closely related but nonidentical genes. We have determined temporal patterns of mRNA accumulation for a large number of collagen genes by screening recombinant phages and plasmids containing cloned collagen genes under high stringency conditions with 32P-labeled cDNA preparations specific for eggs or three postembryonic molts. We find that collagen mRNA levels are regulated both temporally and quantitatively during C. elegans development. Most genes studied exhibit one of four patterns of mRNA accumulation which correlate with changes in cuticle morphology and collagen protein composition during development. Our results suggest that, in general, there is a progressive activation of new collagen genes during normal development.

Stage-specific patterns of collagen gene expression during development of Caenorhabditis elegans

Collagens are the major protein components of the Caenorhabditis elegans cuticle and are encoded by a large family of 40 to 150 closely related but nonidentical genes. We have determined temporal patterns of mRNA accumulation for a large number of collagen genes by screening recombinant phages and plasmids containing cloned collagen genes under high stringency conditions with 32P-labeled cDNA preparations specific for eggs or three postembryonic molts. We find that collagen mRNA levels are regulated both temporally and quantitatively during C. elegans development. Most genes studied exhibit one of four patterns of mRNA accumulation which correlate with changes in cuticle morphology and collagen protein composition during development. Our results suggest that, in general, there is a progressive activation of new collagen genes during normal development.

Isolation and characterization of six different chicken actin genes

Genes representing six different actin isoforms were isolated from a chicken genomic library. Cloned actin cDNAs as well as tissue-specific mRNAs enriched in different actin species were used as hybridization probes to group individual actin genomic clones by their relative thermal stability. Restriction maps showed that these actin genes were derived from separate and nonoverlapping regions of genomic DNA. Of the six isolated genes, five included sequences from both the 5' and 3' ends of the actin-coding area. Amino acid sequence analysis from both the NH2- and COOH-terminal regions provided for the unequivocal identification of these genes. The striated isoforms were represented by the isolated alpha-skeletal, alpha-cardiac, and alpha-smooth muscle actin genes. The nonmuscle isoforms included the beta-cytoplasmic actin gene and an actin gene fragment which lacked the 5' coding and flanking sequence; presumably, this region of DNA was removed from this gene during construction of the genomic library. Unexpectedly, a third nonmuscle chicken actin gene was found which resembled the amphibian type 5 actin isoform (J. Vandekerckhove, W. W. Franke, and K. Weber, J. Mol. Biol., 152:413-426). This nonmuscle actin type has not been previously detected in warm-blooded vertebrates. We showed that interspersed, repeated DNA sequences closely flanked the alpha-skeletal, alpha-cardiac, beta-, and type 5-like actin genes. The repeated DNA sequences which surround the alpha-skeletal actin-coding regions were not related to repetitious DNA located on the other actin genes. Analysis of genomic DNA blots showed that the chicken actin multigene family was represented by 8 to 10 separate coding loci. The six isolated actin genes corresponded to 7 of 11 genomic EcoRI fragments. Only the alpha-smooth muscle actin gene was shown to be split by an EcoRI site. Thus, in the chicken genome each actin isoform appeared to be encoded by a single gene.

Analysis of persistent virus infections by in situ hybridization to whole-mouse sections

Nucleic acid hybridization techniques have contributed significantly to the understanding of gene organization, regulation and expression. In the context of persistent or latent viral infections, hybridization with specific labelled probes represents the most sensitive assay presently available for detection of viral genomes. During the course of persistence, viral genomes may exist in multiple and yet quite segregated areas in an infected host, but examination of all tissues remains difficult and time-consuming. At present, the application of hybridization assays to in vivo infections requires either chemical extraction of nucleic acid coupled with dot-blot and gel transfer techniques or in situ hybridization to cryostat tissue sections. In both cases, selected tissues must be removed by dissection before analysis. We describe here a procedure which allows efficient and reproducible screening of all tissue in an infected host. Our technique allows detection of viral genetic material in whole-body sections of infected mice, and provides the first evidence in vivo for accumulation of viral genetic material with a parallel decrease in infectious virus during persistent virus infection. This technique should be widely applicable to studies of developmental regulation of gene expression, for monitoring locations of gene expression in transgenic mice and for analysis of molecular mechanisms in pathogenesis.

Isolation and characterization of six different chicken actin genes

Genes representing six different actin isoforms were isolated from a chicken genomic library. Cloned actin cDNAs as well as tissue-specific mRNAs enriched in different actin species were used as hybridization probes to group individual actin genomic clones by their relative thermal stability. Restriction maps showed that these actin genes were derived from separate and nonoverlapping regions of genomic DNA. Of the six isolated genes, five included sequences from both the 5' and 3' ends of the actin-coding area. Amino acid sequence analysis from both the NH2- and COOH-terminal regions provided for the unequivocal identification of these genes. The striated isoforms were represented by the isolated alpha-skeletal, alpha-cardiac, and alpha-smooth muscle actin genes. The nonmuscle isoforms included the beta-cytoplasmic actin gene and an actin gene fragment which lacked the 5' coding and flanking sequence; presumably, this region of DNA was removed from this gene during construction of the genomic library. Unexpectedly, a third nonmuscle chicken actin gene was found which resembled the amphibian type 5 actin isoform (J. Vandekerckhove, W. W. Franke, and K. Weber, J. Mol. Biol., 152:413-426). This nonmuscle actin type has not been previously detected in warm-blooded vertebrates. We showed that interspersed, repeated DNA sequences closely flanked the alpha-skeletal, alpha-cardiac, beta-, and type 5-like actin genes. The repeated DNA sequences which surround the alpha-skeletal actin-coding regions were not related to repetitious DNA located on the other actin genes. Analysis of genomic DNA blots showed that the chicken actin multigene family was represented by 8 to 10 separate coding loci. The six isolated actin genes corresponded to 7 of 11 genomic EcoRI fragments. Only the alpha-smooth muscle actin gene was shown to be split by an EcoRI site. Thus, in the chicken genome each actin isoform appeared to be encoded by a single gene.

Regulation of Drosophila alpha- and beta-tubulin genes during development

Both the alpha and the beta subunit of tubulin in Drosophila melanogaster are encoded by small multigene families. Using heterologous hybridization probes representing chicken alpha- and beta-tubulin genes, four complementary alpha- and four beta-tubulin gene sequences from Drosophila have been isolated. Each gene has been individually mapped cytogenically by in situ hybridization of nucleic acid probes to polytene chromosomes. It is clear that the genes in each family are dispersed rather than arranged in tandem arrays or clusters. Furthermore, alpha- and beta-tubulin genes are not physically linked as alpha-beta pairs. Transcripts from individual genes are differentially accumulated at particular stages of Drosophila development. This differential gene activity may provide expression of functionally specialized tubulin subunits. Alternatively, differences in expression may reflect tissue specific patterns of gene utilization.

Molecular cloning of region-specific chorion-encoding RNA sequences

We have constructed a cDNA clone library from poly(A)+ RNA of very-late-period choriogenic silkmoth follicles. Clone DNAs that hybridize preferentially to RNA from the aeropyle crown region of the follicle (versus the flat region) were selected, and all could be placed in one of two homology groups. The two groups represent sequences encoding the very-late-period chorion proteins E1 and E2; this was established by hybrid-selected translation coupled with specific antibody precipitation. Regionalized synthesis of chorion proteins is restricted to the very late period, and its control can now be studied at the nucleic acid level.

Selective detection of rat and mouse specific albumin and alpha-fetoprotein mRNA molecules under highly stringent hybridization conditions

The molecular analysis of some important interactions observed between the parental genomes in interspecific cell hybrids requires the availability of highly specific hybridization assays to selectively quantitate mRNA sequences coding for the same protein but transcribed from the two different genomes. Specific hybridization techniques which should permit the selective detection of rat and mouse albumin and alpha-fetoprotein (AFP) mRNA molecules in a mixture of the two types of mRNAs are presented here. The high degree of homology existing between the AFP mRNA sequences coding for mouse and rat AFP, and, presumably, albumin, results in extensive cross-hybridization with the cDNA probes under standard hybridization conditions. No size differences could be detected between the two types of mRNA molecules from the two species. A Tm difference of 7 degrees C between the intra- and interspecific mRNA:rat cDNA hybrids allowed the establishment of highly stringent solution hybridization conditions necessary to measure separately the contents of rat albumin and AFP mRNAs. Mouse albumin and AFP cDNA clones were then isolated from mouse liver and yolk sac cDNA libraries, and used to show the usefulness of highly stringent washing conditions to discriminate between rat and mouse albumin and AFP mRNA molecules in conventional "Northern blotting" techniques. In combination with the solution hybridization assay, these filter hybridization techniques can be used to specifically quantitate the content of rat and mouse albumin and AFP mRNA molecules in interspecific cell hybrids.

Sequential comparative hybridizations analyzed by computerized image processing can identify and quantitate regulated RNAs

A method to analyze shifts in the relative abundance of many specific RNAs following any stimulus is presented. Hybridizations of two complex "total" cDNA probes (from the pre- and poststimulus states) to each member of a cDNA library are quantitatively analyzed and mathematically compared by using computer-assisted image processing and statistical analysis of sequential filter hybridizations. Experiments indicate that shifts in abundance between two states can be identified and reproducibly quantitated without purified probes. Direct isolation of recombinant cDNA colonies containing inserts corresponding to regulated RNAs is thus possible. The use of this system is demonstrated for partial analysis of the response in vivo of rat liver to glucocorticoids. Application to other biological systems in which a shift between two states occurs is discussed.

Developmental and evolutionary comparisons of proteins from purified ribosomal subunits in two silkmoths

Developmental comparisons of silkmoth ribosomal proteins were performed by parallel two-dimensional electrophoretic analyses of proteins derived from developing adult wings and from ovarian follicles at the prechoriogenic and choriogenic stages of development (before and during secretion of the chorion, respectively). Proteins of 40S and 60S subunits were prepared and analyzed separately. A single major developmental difference was observed, exclusively in choriogenic follicles: the majority of a 40S subunit protein, S6, was shifted to a more acidic form, possibly as a result of phosphorylation. A less prominent change was apparently due to quantitative variation between two forms of one large subunit protein. The developmental comparisons were performed in two species of the genus Antheraea, with consistent results. Comparisons between the two species revealed remarkable evolutionary conservation of the ribosomal protein patterns, sharply contrasting with the evolutionary diversification of chorion structural proteins in the same two species. The only detectable interspecies differences in ribosomal components were (a) slightly more acidic behaviour of one small-subunit protein and more basic behaviour of one large-subunit protein in Antheraea polyphemus as compared to Antheraea pernyi, and (b) presence of an apparently species-specific 60 S subunit protein in A. pernyi, which in A. polyphemus probably co-migrates with a neighbouring protein.

The B multigene family of chorion proteins in saturniid silkmoths

The main features of the B family of chorion proteins in saturniid moths were examined by partial sequencing of representative B proteins, seven from Antheraea polyphemus and two from A. pernyi. Comparisons were made to sequences derived from seven recombinant DNA clones representing three types of B family proteins of A. polyphemus. The central regions of the sequences are conservative, both within and between moth species, and differ largely by a few amino acid replacements, rather than deletions or insertions. By contrast, the amino-terminal third varies more substantially, in a manner which defines two protein subfamilies: within each subfamily sequences are similar, but the subfamilies differ by at least two multiresidue deletions as well as by amino acid replacements. These properties are analogous to features of the A family of chorion proteins.

Novel B family sequence from an early chorion cDNA library of Bombyx mori

A cDNA library has been constructed from transcripts present during the early stages of choriogenesis in the silk-moth, Bombyx mori. Clones representing novel sequences were selected by screening the library with (i) homotypic cDNA, (ii) rDNA and typical chorion probes of the A and B multigene families and (iii) selected clones from the library, which were positive in step (i) but negative in step (ii); this third step identified clones that hybridized to distinct subsets of the library. The sequence of one such clone was determined and shown to represent a novel subfamily of the B chorion multigene family, exclusively expressed during the early choriogenic period.

Spot blot: a hybridization assay for specific DNA sequences in multiple samples

Small aliquots of DNA-containing samples from gradient or column fractions are spotted onto agarose plates containing ethidium bromide, and the DNA is visualized qualitatively. After it is overlaid with a thin agarose cover, the DNA is denatured and transferred to nitrocellulose filters for hybridization. This method, called the "spot-blot assay," is particularly convenient when dealing with large numbers of samples.

Silkmoth chorion multigene families constitute a superfamily: comparison of C and B family sequences

We have characterized a new family of silkmoth chorion genes, called C, which is distinct from previously characterized A and B families. The amino acid compositions of 18 purified C proteins have been determined. Three subgroups are recognized on the basis of compositional similarities and may correspond to distinct gene families or subfamilies. The sequences of two overlapping cDNA clones have been determined in their entirety and shown to correspond to a C-specific sequence. Obvious homology is observed between the middle portions of the C sequence and previously characterized B sequences. By contrast, the arms of the C sequence share no significant similarities either with each other or with the corresponding arms of B sequences. Thus, the same tripartite structure originally observed in A and B family sequences is also present in the C family and may have functional significance. Secondary structure prediction of the C sequence is presented and supports this conclusion. The observed homology between C and B family sequences clearly establishes that silkmoth chorion multigene families constitute a superfamily.

Keratin gene expression in mouse epidermis and cultured epidermal cells

The major differentiation products of mouse epidermis are keratins of 40-70 kilodaltons (kDal). We have prepared a library of cDNA clones from total poly(A)+ RNA from newborn mouse epidermis. Clones corresponding to the major in vivo keratins of 55, 59, and 67 kDal have been isolated and characterized. By RNA blot analysis of poly(A)+ RNA from newborn mouse epidermis, we have identified RNA species that are approximately 1,600, 2,000, and 2,400 nucleotides in length and are complementary to the cDNAs for the 55-, 59-, and 67-kDal keratins, respectively. Analysis of RNA from primary cultures of newborn mouse epidermis by this same technique shows greatly reduced levels of these RNAs. Transcripts complementary to all three cloned cDNAs are abundant in 14- to 16-day embryonic and adult mouse skin. Thus, altered expression in culture does not appear to be due to induction of a developmentally programmed switch by placing the cells in culture but instead is due to factors modulating expression within the culture system. Because the 55-, 59-, and 67-kDal keratins are the major proteins in epidermis they probably represent keratin associated with terminal differentiation. The expression data suggest that cultured cells are blocked in expression of differentiation keratins but instead synthesize other keratin family members probably related to cytoskeletal functions.

Use of a cDNA library for the study of mRNA changes during muscle differentiation

A cDNA library was used to measure changes in many individual mRNAs during muscle differentiation in culture. A library of 1000 clones was constructed from total myofiber poly(A) RNA. About 23% of these clones gave a detectable colony hybridization signal using end-labeled myofiber mRNA, the remainder containing muscle sequences too rare to be detected with this assay. The 230 positive clones were grouped into four classes based on relative visual intensity. Reconstruction experiments using pure globin mRNA enable us to determine the approximate percentage of total RNA made up by each mRNA hybridizing to a cDNA clone. Those clones containing sequences complementary to developmentally regulated mRNAs were identified by a differential hybridization procedure. The cDNA library was screened with end-labeled mRNA from both undifferentiated myoblasts and differentiated myofibers. Although the bulk of the clones hybridized essentially the same with both RNA populations, several dozen were found which hybridized differentially. Some clones contained sequences which were not present at all in myoblasts and present in very high quantities in myofibers. Others contained sequences found in both myoblasts and myofibers but in increased quantities in the differentiated cells. Still others contained sequences which decreased in quantity during muscle differentiation. The clones in the first group were chosen for immediate analysis since they likely contain contractile protein mRNA sequences. However, all the characterized cDNA clones can now be used as probes to study the chromosomal organization and developmental expression of genes active during muscle differentiation.

Accepted mutations in a gene family: evolutionary diversification of duplicated DNA

We report and compare the DNA sequences of 14 silkmoth (Antheraea polyphemus) chorion genes, derived from either cDNA or chromosomal DNA clones. Seven of these genes are members of the A multigene family, and seven are members of the B family. Where available, the previously reported (Jones and Kafatos 1980) intronic and extragenic flanking DNA sequences are also considered. Closely related sequences are compared, revealing the types of spontaneous mutations that were fixed during paralogous evolution. Segmental mutations (i.e. mutations other than substitutions) are nearly always interpretable as small duplications or deletions, related to small direct repeats. Segmental mutations are strongly constrained in the coding regions, although they do occur. Nucleotide substitutions also appear to be under selective constraints: relatively few substitutions leading to amino acid replacements are accepted, silent substitutions leading to some codons (especially purine-terminated ones) are disfavored, and different compositional biases are maintained in different parts of the sequences. Other sequence differences can be interpreted as indicative of neutral drift, including most differences in non-coding regions and most T/C transitions in third-base positions. In the non-coding regions, which are thought to be only loosely constrained by selection, transitions are observed more frequently than might be expected: they account for 52% of all substitutions, and they appear to be favored two to threefold over transversions when allowance is made for the skewed base composition of these regions.

Evolution of a multigene family of chorion proteins in silkmoths

The evolution of the A family of chorion genes was examined by comparing new protein and DNA sequences from the silkmoths Antheraea pernyi and Bombyx mori with previously known sequences from Antheraea polyphemus. The comparisons indicated that the A family and its major subfamilies are ancient and revealed how parts of the genes corresponding to distinct regions of the protein structure have evolved, both by base substitutions and by segmental reduplications and deletions.